diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index c2b511c2672..3669d0d88ef 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -17,7 +17,6 @@ outputs: total_shards: description: "Total number of shards" value: ${{ steps.shards.outputs.total_shards }} - runs: using: "composite" steps: @@ -26,22 +25,24 @@ runs: with: version: ${{ env.NFT_VER }} install-pdiff: true - - name: Get number of shards id: shards shell: bash run: | - # Prepare tag parameter if tags are provided TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "") - # Run nf-test with dynamic tag parameter + + # Run nf-test with dynamic parameter nftest_output=$(nf-test test \ --dry-run \ --profile docker \ ${TAGS} \ --filter process,workflow \ - ${{ inputs.paths }}) - + ${{ inputs.paths }}) || { + echo "nf-test command failed with exit code $?" + echo "Full output: $nftest_output" + exit 1 + } echo "nf-test dry-run output: $nftest_output" # Default values for shard and total_shards diff --git a/.github/scripts/conda_env_sorter.py b/.github/scripts/conda_env_sorter.py new file mode 100755 index 00000000000..2c020fffe9c --- /dev/null +++ b/.github/scripts/conda_env_sorter.py @@ -0,0 +1,119 @@ +#!/usr/bin/env python3 +# /// script +# requires-python = ">=3.10" +# dependencies = [ +# "ruamel.yaml", +# ] +# /// + +"""Sort dependencies in conda environment files.""" +# Test with +# uv run --with pytest -- pytest -v .github/scripts/conda_env_sorter.py + +import argparse +import sys +from pathlib import Path +from typing import Optional, Sequence + +import ruamel.yaml + +# Add pytest imports conditionally +if "pytest" in sys.modules: + import pytest + +yaml = ruamel.yaml.YAML() +yaml.indent(mapping=2, sequence=2, offset=2) # Set indentation to 2 spaces + + +def main(argv: Optional[Sequence[str]] = None) -> None: + """Sort dependencies in conda environment files.""" + parser = argparse.ArgumentParser() + parser.add_argument("paths", nargs="*", type=Path) + args = parser.parse_args(argv) + for path in args.paths: + # Read the entire file content + with path.open() as f: + lines = f.readlines() + + # Define the schema lines to be added if missing + schema_lines = [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ] + + # Check if the first two lines match the expected schema lines + if lines[:2] == schema_lines: + content = "".join(lines[2:]) # Skip schema lines when reading content + else: + content = "".join(lines) # Use all content if no schema lines present + + # Parse the YAML content + doc = yaml.load(content) + dicts = [] + others = [] + + for term in doc["dependencies"]: + if isinstance(term, dict): + dicts.append(term) + else: + others.append(term) + others.sort(key=str) + for dict_term in dicts: + for value in dict_term.values(): + if isinstance(value, list): + value.sort(key=str) + dicts.sort(key=str) + doc["dependencies"].clear() + doc["dependencies"].extend(others) + doc["dependencies"].extend(dicts) + + # Write back to file with headers + with path.open("w") as f: + # Always write schema lines first + f.writelines(schema_lines) + # Then dump the sorted YAML + yaml.dump(doc, f) + + +if __name__ == "__main__": + main() + +# Pytest tests (only loaded when running pytest) +if "pytest" in sys.modules: + + @pytest.mark.parametrize( + "input_content,expected", + [ + # Test basic sorting + ("dependencies:\n - zlib\n - python\n", ["python", "zlib"]), + # Test dict sorting + ("dependencies:\n - pip:\n - b\n - a\n - python\n", ["python", {"pip": ["a", "b"]}]), + # Test existing headers + ("---\n# yaml-language-server: $schema=...\ndependencies:\n - b\n - a\n", ["a", "b"]), + ], + ) + def test_conda_sorter(tmp_path, input_content, expected): + test_file = tmp_path / "environment.yml" + test_file.write_text(input_content) + + # Run our sorter on the test file + main([str(test_file)]) + + # Read back the sorted file + result = test_file.read_text() + + # Check schema headers are present + assert result.startswith("---\n# yaml-language-server: $schema=") + + # Parse the sorted content (skip first 2 header lines) + parsed = yaml.load("".join(result.splitlines(True)[2:])) + + # Compare the actual dependencies structure + assert parsed["dependencies"] == expected + + def test_invalid_file(tmp_path): + test_file = tmp_path / "bad.yml" + test_file.write_text("invalid: yaml: here") + + with pytest.raises(ruamel.yaml.scanner.ScannerError): + main([str(test_file)]) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 7417d0961b7..289b55084fd 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -193,3 +193,11 @@ jobs: echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "DEBUG: needs.nf-test.outputs.filtered_paths = ${{ needs.nf-test.outputs.filtered_paths }}" echo "::endgroup::" + + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + if: always() + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 11b6c01adf5..f43586e693c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,13 @@ repos: + - repo: local + hooks: + - id: conda-env-sorter + name: Sort dependencies in conda environment files. + entry: ./.github/scripts/conda_env_sorter.py + language: python + files: environment + types: [yaml] + additional_dependencies: ["ruamel.yaml"] - repo: https://github.com/pre-commit/mirrors-prettier rev: "v3.1.0" hooks: diff --git a/modules/nf-core/abacas/environment.yml b/modules/nf-core/abacas/environment.yml index a3e0eb8d415..109383731f3 100644 --- a/modules/nf-core/abacas/environment.yml +++ b/modules/nf-core/abacas/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml index c7a7d19971f..53fe98570a2 100644 --- a/modules/nf-core/abricate/run/environment.yml +++ b/modules/nf-core/abricate/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/abricate/summary/environment.yml b/modules/nf-core/abricate/summary/environment.yml index c7a7d19971f..53fe98570a2 100644 --- a/modules/nf-core/abricate/summary/environment.yml +++ b/modules/nf-core/abricate/summary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/abritamr/run/environment.yml b/modules/nf-core/abritamr/run/environment.yml index a7c8d047fd1..c9ed91ab0b8 100644 --- a/modules/nf-core/abritamr/run/environment.yml +++ b/modules/nf-core/abritamr/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/adapterremoval/environment.yml b/modules/nf-core/adapterremoval/environment.yml index 0e089bfb305..24e78cdb10d 100644 --- a/modules/nf-core/adapterremoval/environment.yml +++ b/modules/nf-core/adapterremoval/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/adapterremovalfixprefix/environment.yml b/modules/nf-core/adapterremovalfixprefix/environment.yml index b682ca4baa7..c3539cc286b 100644 --- a/modules/nf-core/adapterremovalfixprefix/environment.yml +++ b/modules/nf-core/adapterremovalfixprefix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/admixture/environment.yml b/modules/nf-core/admixture/environment.yml index 30cac0d6b09..d2a8cb1827e 100644 --- a/modules/nf-core/admixture/environment.yml +++ b/modules/nf-core/admixture/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml index 6f25cb2ae1c..1b7707e9fd1 100644 --- a/modules/nf-core/affy/justrma/environment.yml +++ b/modules/nf-core/affy/justrma/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agat/convertbed2gff/environment.yml b/modules/nf-core/agat/convertbed2gff/environment.yml index 2c3daab3437..07256589467 100644 --- a/modules/nf-core/agat/convertbed2gff/environment.yml +++ b/modules/nf-core/agat/convertbed2gff/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::agat=1.4.2" + - bioconda::agat=1.4.2 diff --git a/modules/nf-core/agat/convertspgff2gtf/environment.yml b/modules/nf-core/agat/convertspgff2gtf/environment.yml index d9cd916872b..07256589467 100644 --- a/modules/nf-core/agat/convertspgff2gtf/environment.yml +++ b/modules/nf-core/agat/convertspgff2gtf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agat/convertspgff2tsv/environment.yml b/modules/nf-core/agat/convertspgff2tsv/environment.yml index d9cd916872b..07256589467 100644 --- a/modules/nf-core/agat/convertspgff2tsv/environment.yml +++ b/modules/nf-core/agat/convertspgff2tsv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml index d9cd916872b..07256589467 100644 --- a/modules/nf-core/agat/convertspgxf2gxf/environment.yml +++ b/modules/nf-core/agat/convertspgxf2gxf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agat/spaddintrons/environment.yml b/modules/nf-core/agat/spaddintrons/environment.yml index 9c14047a91d..07256589467 100644 --- a/modules/nf-core/agat/spaddintrons/environment.yml +++ b/modules/nf-core/agat/spaddintrons/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::agat=1.4.2" + - bioconda::agat=1.4.2 diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml index 2c3daab3437..07256589467 100644 --- a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml +++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::agat=1.4.2" + - bioconda::agat=1.4.2 diff --git a/modules/nf-core/agat/spmergeannotations/environment.yml b/modules/nf-core/agat/spmergeannotations/environment.yml index 2c3daab3437..07256589467 100644 --- a/modules/nf-core/agat/spmergeannotations/environment.yml +++ b/modules/nf-core/agat/spmergeannotations/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::agat=1.4.2" + - bioconda::agat=1.4.2 diff --git a/modules/nf-core/agat/spstatistics/environment.yml b/modules/nf-core/agat/spstatistics/environment.yml index d9cd916872b..07256589467 100644 --- a/modules/nf-core/agat/spstatistics/environment.yml +++ b/modules/nf-core/agat/spstatistics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agat/sqstatbasic/environment.yml b/modules/nf-core/agat/sqstatbasic/environment.yml index d9cd916872b..07256589467 100644 --- a/modules/nf-core/agat/sqstatbasic/environment.yml +++ b/modules/nf-core/agat/sqstatbasic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/agrvate/environment.yml b/modules/nf-core/agrvate/environment.yml index bfdd71d2968..dfd9601911f 100644 --- a/modules/nf-core/agrvate/environment.yml +++ b/modules/nf-core/agrvate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ale/environment.yml b/modules/nf-core/ale/environment.yml index 566c1d72404..dc5a46e0653 100644 --- a/modules/nf-core/ale/environment.yml +++ b/modules/nf-core/ale/environment.yml @@ -6,4 +6,4 @@ channels: - tanghaibao dependencies: # renovate: datasource=conda depName=bioconda/ale - - "bioconda::ale=20180904" + - bioconda::ale=20180904 diff --git a/modules/nf-core/allelecounter/environment.yml b/modules/nf-core/allelecounter/environment.yml index 69179cbf949..8090e8bb85e 100644 --- a/modules/nf-core/allelecounter/environment.yml +++ b/modules/nf-core/allelecounter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml index 1e945daa712..976ede7d6a1 100644 --- a/modules/nf-core/ampcombi/environment.yml +++ b/modules/nf-core/ampcombi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ampcombi2/cluster/environment.yml b/modules/nf-core/ampcombi2/cluster/environment.yml index f9c25b04a1d..e88b26ba05f 100644 --- a/modules/nf-core/ampcombi2/cluster/environment.yml +++ b/modules/nf-core/ampcombi2/cluster/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ampcombi=2.0.1" + - bioconda::ampcombi=2.0.1 diff --git a/modules/nf-core/ampcombi2/complete/environment.yml b/modules/nf-core/ampcombi2/complete/environment.yml index f9c25b04a1d..e88b26ba05f 100644 --- a/modules/nf-core/ampcombi2/complete/environment.yml +++ b/modules/nf-core/ampcombi2/complete/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ampcombi=2.0.1" + - bioconda::ampcombi=2.0.1 diff --git a/modules/nf-core/ampcombi2/parsetables/environment.yml b/modules/nf-core/ampcombi2/parsetables/environment.yml index f9c25b04a1d..e88b26ba05f 100644 --- a/modules/nf-core/ampcombi2/parsetables/environment.yml +++ b/modules/nf-core/ampcombi2/parsetables/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ampcombi=2.0.1" + - bioconda::ampcombi=2.0.1 diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml index 359e426c508..3c6f4793f85 100644 --- a/modules/nf-core/ampir/environment.yml +++ b/modules/nf-core/ampir/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml index e1cb57035ec..872115b4514 100644 --- a/modules/nf-core/amplify/predict/environment.yml +++ b/modules/nf-core/amplify/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/amps/environment.yml b/modules/nf-core/amps/environment.yml index d78219cbe01..a1a3b3a2b2c 100644 --- a/modules/nf-core/amps/environment.yml +++ b/modules/nf-core/amps/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml index 2744ce54420..0487b72de5b 100644 --- a/modules/nf-core/amrfinderplus/run/environment.yml +++ b/modules/nf-core/amrfinderplus/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml index 2744ce54420..0487b72de5b 100644 --- a/modules/nf-core/amrfinderplus/update/environment.yml +++ b/modules/nf-core/amrfinderplus/update/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/angsd/contamination/environment.yml b/modules/nf-core/angsd/contamination/environment.yml index f2f4e7d3d77..d3d86d4d28e 100644 --- a/modules/nf-core/angsd/contamination/environment.yml +++ b/modules/nf-core/angsd/contamination/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/angsd/docounts/environment.yml b/modules/nf-core/angsd/docounts/environment.yml index 3f1bb661cf2..395b34e8daa 100644 --- a/modules/nf-core/angsd/docounts/environment.yml +++ b/modules/nf-core/angsd/docounts/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/angsd/gl/environment.yml b/modules/nf-core/angsd/gl/environment.yml index 6e7fda79f94..d8f4fb998e2 100644 --- a/modules/nf-core/angsd/gl/environment.yml +++ b/modules/nf-core/angsd/gl/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::angsd=0.940" - - "bioconda::htslib=1.17" + - bioconda::angsd=0.940 + - bioconda::htslib=1.17 diff --git a/modules/nf-core/anndata/barcodes/environment.yml b/modules/nf-core/anndata/barcodes/environment.yml index b43edd6c7ae..cb4494f6d7e 100644 --- a/modules/nf-core/anndata/barcodes/environment.yml +++ b/modules/nf-core/anndata/barcodes/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/anndata/getsize/environment.yml b/modules/nf-core/anndata/getsize/environment.yml index b43edd6c7ae..cb4494f6d7e 100644 --- a/modules/nf-core/anndata/getsize/environment.yml +++ b/modules/nf-core/anndata/getsize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml index 6b6608d440b..428ac6f65d5 100644 --- a/modules/nf-core/annotsv/annotsv/environment.yml +++ b/modules/nf-core/annotsv/annotsv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/annotsv/installannotations/environment.yml b/modules/nf-core/annotsv/installannotations/environment.yml index 6b6608d440b..428ac6f65d5 100644 --- a/modules/nf-core/annotsv/installannotations/environment.yml +++ b/modules/nf-core/annotsv/installannotations/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/anota2seq/anota2seqrun/environment.yml b/modules/nf-core/anota2seq/anota2seqrun/environment.yml index a0b0b3180f8..9094a26b9e9 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/environment.yml +++ b/modules/nf-core/anota2seq/anota2seqrun/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-anota2seq=1.24.0" + - bioconda::bioconductor-anota2seq=1.24.0 diff --git a/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r b/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r index 82fef8d8346..aaa4e3d383a 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r +++ b/modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r @@ -327,12 +327,11 @@ ads <- do.call(anota2seqDataSetFromMatrix, anota2seqDataSetFromMatrix_args) # Run anota2seqRun contrast_matrix <- matrix( - nrow=2, - ncol=1, - dimnames=list(c(opt\$reference_level, opt\$target_level),c()), - c(-1,1) + c(-1, 1), + nrow = 2, + dimnames = list(sort(c(opt\$reference_level, opt\$target_level)), NULL) ) - + ads <- anota2seqRun( ads, contrasts = contrast_matrix, diff --git a/modules/nf-core/antismash/antismashlite/environment.yml b/modules/nf-core/antismash/antismashlite/environment.yml index ce4491dc556..dc2807d59b9 100644 --- a/modules/nf-core/antismash/antismashlite/environment.yml +++ b/modules/nf-core/antismash/antismashlite/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf index 422e7be0499..3a5215575cb 100644 --- a/modules/nf-core/antismash/antismashlite/main.nf +++ b/modules/nf-core/antismash/antismashlite/main.nf @@ -1,44 +1,45 @@ process ANTISMASH_ANTISMASHLITE { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/antismash-lite:7.1.0--pyhdfd78af_0' : - 'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/antismash-lite:7.1.0--pyhdfd78af_0' + : 'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0'}" containerOptions { - workflow.containerEngine == 'singularity' ? - "-B $antismash_dir:/usr/local/lib/python3.10/site-packages/antismash" : - workflow.containerEngine == 'docker' ? - "-v \$PWD/$antismash_dir:/usr/local/lib/python3.10/site-packages/antismash" : - '' - } + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? "-B ${antismash_dir}:/usr/local/lib/python3.10/site-packages/antismash" + : workflow.containerEngine == 'docker' + ? "-v \$PWD/${antismash_dir}:/usr/local/lib/python3.10/site-packages/antismash" + : '' + } input: tuple val(meta), path(sequence_input) - path(databases) - path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml). - path(gff) + path databases + path antismash_dir + // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml). + path gff output: - tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file - tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files - tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html - tuple val(meta), path("${prefix}/knownclusterblast/") , optional: true, emit: knownclusterblast_dir - tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt - tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast - tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast - tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input - tuple val(meta), path("${prefix}/*.json") , emit: json_results - tuple val(meta), path("${prefix}/*.log") , emit: log - tuple val(meta), path("${prefix}/*.zip") , emit: zip - tuple val(meta), path("${prefix}/*region*.gbk") , optional: true, emit: gbk_results - tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput - tuple val(meta), path("${prefix}/index.html") , emit: html - tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput - tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}/clusterblast/*_c*.txt"), optional: true, emit: clusterblast_file + tuple val(meta), path("${prefix}/{css,images,js}"), emit: html_accessory_files + tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html"), optional: true, emit: knownclusterblast_html + tuple val(meta), path("${prefix}/knownclusterblast/"), optional: true, emit: knownclusterblast_dir + tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt"), optional: true, emit: knownclusterblast_txt + tuple val(meta), path("${prefix}/svg/clusterblast*.svg"), optional: true, emit: svg_files_clusterblast + tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg"), optional: true, emit: svg_files_knownclusterblast + tuple val(meta), path("${prefix}/*.gbk"), emit: gbk_input + tuple val(meta), path("${prefix}/*.json"), emit: json_results + tuple val(meta), path("${prefix}/*.log"), emit: log + tuple val(meta), path("${prefix}/*.zip"), emit: zip + tuple val(meta), path("${prefix}/*region*.gbk"), optional: true, emit: gbk_results + tuple val(meta), path("${prefix}/clusterblastoutput.txt"), optional: true, emit: clusterblastoutput + tuple val(meta), path("${prefix}/index.html"), emit: html + tuple val(meta), path("${prefix}/knownclusterblastoutput.txt"), optional: true, emit: knownclusterblastoutput + tuple val(meta), path("${prefix}/regions.js"), emit: json_sideloading + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -53,25 +54,24 @@ process ANTISMASH_ANTISMASHLITE { ## this should be run as a separate module for versioning purposes antismash \\ - $args \\ - $gff_flag \\ - -c $task.cpus \\ - --output-dir $prefix \\ - --output-basename $prefix \\ + ${args} \\ + ${gff_flag} \\ + -c ${task.cpus} \\ + --output-dir ${prefix} \\ + --output-basename ${prefix} \\ --genefinding-tool none \\ - --logfile $prefix/${prefix}.log \\ - --databases $databases \\ - $sequence_input + --logfile ${prefix}/${prefix}.log \\ + --databases ${databases} \\ + ${sequence_input} cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //') + antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g') END_VERSIONS """ stub: prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" - def VERSION = '7.1.0' // WARN: Version information not provided by tool during stub run. Please update this string when bumping container versions. """ mkdir -p ${prefix}/css mkdir ${prefix}/images @@ -91,7 +91,7 @@ process ANTISMASH_ANTISMASHLITE { cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash-lite: $VERSION + antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g') END_VERSIONS """ } diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test b/modules/nf-core/antismash/antismashlite/tests/main.nf.test index 5ee21d6ded4..d58fcc4c910 100644 --- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test +++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process ANTISMASH_ANTISMASHLITE" script "../main.nf" process "ANTISMASH_ANTISMASHLITE" + config './nextflow.config' tag "modules" tag "modules_nfcore" @@ -96,7 +97,11 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).text.contains("https://antismash.secondarymetabolites.org/") }, { assert path(process.out.json_sideloading.get(0).get(1)).text.contains("\"seq_id\": \"NZ_CP069563.1\"") }, { assert path(process.out.log.get(0).get(1)).text.contains("antiSMASH status: SUCCESS") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + path(process.out.versions[0]).yaml, + file(process.out.versions[0]).name, + ).match("versions") + } ) } } @@ -119,7 +124,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.versions[0]).name, + ).match("versions_stub") + } ) } } diff --git a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap index 618b06f965a..7d2febc93f7 100644 --- a/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap @@ -1,15 +1,28 @@ { + "versions_stub": { + "content": [ + "versions.yml" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-30T14:55:41.041351955" + }, "versions": { "content": [ - [ - "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" - ] + { + "ANTISMASH_ANTISMASHLITE": { + "antismash-lite": "7.1.0" + } + }, + "versions.yml" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-09T17:06:08.439031477" + "timestamp": "2025-01-30T13:48:51.158220245" }, "html_accessory_files": { "content": [ @@ -64,238 +77,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-09T17:06:08.392236617" - }, - "antismashlite - bacteroides_fragilis - genome - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - [ - [ - "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "10": [ - [ - { - "id": "test" - }, - "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "11": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "12": [ - - ], - "13": [ - [ - { - "id": "test" - }, - "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "14": [ - - ], - "15": [ - [ - { - "id": "test" - }, - "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "16": [ - "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "8": [ - [ - { - "id": "test" - }, - "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "9": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "clusterblast_file": [ - - ], - "clusterblastoutput": [ - - ], - "gbk_input": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "gbk_results": [ - [ - { - "id": "test" - }, - [ - "NZ_CP069563.1.region001.gbk:md5,d41d8cd98f00b204e9800998ecf8427e", - "NZ_CP069563.1.region002.gbk:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "html": [ - [ - { - "id": "test" - }, - "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "html_accessory_files": [ - [ - { - "id": "test" - }, - [ - [ - "bacteria.css:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "about.svg:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "antismash.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "json_results": [ - [ - { - "id": "test" - }, - "genome.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json_sideloading": [ - [ - { - "id": "test" - }, - "regions.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "knownclusterblast_dir": [ - - ], - "knownclusterblast_html": [ - - ], - "knownclusterblast_txt": [ - - ], - "knownclusterblastoutput": [ - - ], - "log": [ - [ - { - "id": "test" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "svg_files_clusterblast": [ - - ], - "svg_files_knownclusterblast": [ - - ], - "versions": [ - "versions.yml:md5,2a1c54c017741b59c057a05453fc067d" - ], - "zip": [ - [ - { - "id": "test" - }, - "genome.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-07-11T16:35:51.079804" + "timestamp": "2025-01-30T14:47:32.466485783" } } \ No newline at end of file diff --git a/modules/nf-core/antismash/antismashlite/tests/nextflow.config b/modules/nf-core/antismash/antismashlite/tests/nextflow.config new file mode 100644 index 00000000000..eedb39ae891 --- /dev/null +++ b/modules/nf-core/antismash/antismashlite/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: ANTISMASH_ANTISMASHLITE { + memory = 7.GB + } +} diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml index ce4491dc556..dc2807d59b9 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf index e63f20d2ea6..52452dc279e 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf @@ -2,9 +2,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/antismash-lite:7.1.0--pyhdfd78af_0' : - 'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/antismash-lite:7.1.0--pyhdfd78af_0' + : 'biocontainers/antismash-lite:7.1.0--pyhdfd78af_0'}" /* These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH. @@ -13,12 +13,12 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { */ containerOptions { - workflow.containerEngine == 'singularity' ? - "-B $database_css:/usr/local/lib/python3.10/site-packages/antismash/outputs/html/css,$database_detection:/usr/local/lib/python3.10/site-packages/antismash/detection,$database_modules:/usr/local/lib/python3.10/site-packages/antismash/modules" : - workflow.containerEngine == 'docker' ? - "-v \$PWD/$database_css:/usr/local/lib/python3.10/site-packages/antismash/outputs/html/css -v \$PWD/$database_detection:/usr/local/lib/python3.10/site-packages/antismash/detection -v \$PWD/$database_modules:/usr/local/lib/python3.10/site-packages/antismash/modules" : - '' - } + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? "-B ${database_css}:/usr/local/lib/python3.10/site-packages/antismash/outputs/html/css,${database_detection}:/usr/local/lib/python3.10/site-packages/antismash/detection,${database_modules}:/usr/local/lib/python3.10/site-packages/antismash/modules" + : workflow.containerEngine == 'docker' + ? "-v \$PWD/${database_css}:/usr/local/lib/python3.10/site-packages/antismash/outputs/html/css -v \$PWD/${database_detection}:/usr/local/lib/python3.10/site-packages/antismash/detection -v \$PWD/${database_modules}:/usr/local/lib/python3.10/site-packages/antismash/modules" + : '' + } input: path database_css @@ -26,8 +26,8 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { path database_modules output: - path("antismash_db") , emit: database - path("antismash_dir"), emit: antismash_dir + path ("antismash_db"), emit: database + path ("antismash_dir"), emit: antismash_dir path "versions.yml", emit: versions when: @@ -35,35 +35,34 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { script: def args = task.ext.args ?: '' - cp_cmd = ( session.config.conda && session.config.conda.enabled ) ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.10/site-packages/antismash antismash_dir;" + cp_cmd = session.config.conda && session.config.conda.enabled ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.10/site-packages/antismash antismash_dir;" """ download-antismash-databases \\ --database-dir antismash_db \\ - $args + ${args} - $cp_cmd + ${cp_cmd} cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash-lite: \$(antismash --version | sed 's/antiSMASH //') + antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g') END_VERSIONS """ stub: def args = task.ext.args ?: '' - cp_cmd = (session.config.conda && session.config.conda.enabled ) ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.10/site-packages/antismash antismash_dir;" - def VERSION = '7.1.0' // WARN: Version information not provided by tool during stub run. Please update this string when bumping container versions. + cp_cmd = session.config.conda && session.config.conda.enabled ? "cp -r \$(python -c 'import antismash;print(antismash.__file__.split(\"/__\")[0])') antismash_dir;" : "cp -r /usr/local/lib/python3.10/site-packages/antismash antismash_dir;" """ - echo "download-antismash-databases --database-dir antismash_db $args" + echo "download-antismash-databases --database-dir antismash_db ${args}" - echo "$cp_cmd" + echo "${cp_cmd}" mkdir antismash_dir mkdir antismash_db cat <<-END_VERSIONS > versions.yml "${task.process}": - antismash-lite: $VERSION + antismash-lite: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g') END_VERSIONS """ } diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test index 55f5f2f50a1..72e5d7dd833 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES" script "../main.nf" process "ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES" + config './nextflow.config' tag "modules" tag "modules_nfcore" @@ -64,10 +65,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot ( + { assert snapshot( file(process.out.database.get(0)).list().sort(), - process.out.versions, - ).match() } + path(process.out.versions[0]).yaml, + file(process.out.versions[0]).name, + ).match() + } ) } } @@ -128,7 +131,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.database.get(0)).list().sort(), + file(process.out.versions[0]).name, + ).match() + } ) } } diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap index 21ee9d410f5..04f98af8497 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap @@ -1,40 +1,16 @@ { "antiSMASH-lite downloaddatabases - stub": { "content": [ - { - "0": [ - [ - - ] - ], - "1": [ - [ - - ] - ], - "2": [ - "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" - ], - "antismash_dir": [ - [ - - ] - ], - "database": [ - [ - - ] - ], - "versions": [ - "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" - ] - } + [ + + ], + "versions.yml" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-07-12T13:41:29.456143" + "timestamp": "2025-01-30T13:47:43.854140981" }, "antiSMASH-lite downloaddatabases": { "content": [ @@ -49,14 +25,17 @@ "resfam", "tigrfam" ], - [ - "versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a" - ] + { + "ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES": { + "antismash-lite": "7.1.0" + } + }, + "versions.yml" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-07-12T13:41:08.116244" + "timestamp": "2025-01-30T13:57:10.845020955" } } \ No newline at end of file diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/nextflow.config b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/nextflow.config new file mode 100644 index 00000000000..972dd7b04f2 --- /dev/null +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES { + memory = 7.GB + } +} diff --git a/modules/nf-core/arcashla/extract/environment.yml b/modules/nf-core/arcashla/extract/environment.yml index f5cd15eabc1..de34c44d2cd 100644 --- a/modules/nf-core/arcashla/extract/environment.yml +++ b/modules/nf-core/arcashla/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/argnorm/environment.yml b/modules/nf-core/argnorm/environment.yml index 783995f288c..9197100139a 100644 --- a/modules/nf-core/argnorm/environment.yml +++ b/modules/nf-core/argnorm/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::argnorm=0.5.0" + - bioconda::argnorm=0.5.0 diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml index 52d11ba96ba..4536048c73d 100644 --- a/modules/nf-core/aria2/environment.yml +++ b/modules/nf-core/aria2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ariba/getref/environment.yml b/modules/nf-core/ariba/getref/environment.yml index 49af201aa81..94c39c99332 100644 --- a/modules/nf-core/ariba/getref/environment.yml +++ b/modules/nf-core/ariba/getref/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ariba/run/environment.yml b/modules/nf-core/ariba/run/environment.yml index 49af201aa81..94c39c99332 100644 --- a/modules/nf-core/ariba/run/environment.yml +++ b/modules/nf-core/ariba/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/arriba/download/environment.yml b/modules/nf-core/arriba/download/environment.yml index d0883a0d205..e8f5b278fe8 100644 --- a/modules/nf-core/arriba/download/environment.yml +++ b/modules/nf-core/arriba/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/art/illumina/environment.yml b/modules/nf-core/art/illumina/environment.yml index eedc114c662..3e92aa614fe 100644 --- a/modules/nf-core/art/illumina/environment.yml +++ b/modules/nf-core/art/illumina/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/artic/guppyplex/environment.yml b/modules/nf-core/artic/guppyplex/environment.yml index cf5ae4cf5c5..fd739b2cf0d 100644 --- a/modules/nf-core/artic/guppyplex/environment.yml +++ b/modules/nf-core/artic/guppyplex/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/artic/minion/environment.yml b/modules/nf-core/artic/minion/environment.yml index cf5ae4cf5c5..fd739b2cf0d 100644 --- a/modules/nf-core/artic/minion/environment.yml +++ b/modules/nf-core/artic/minion/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ascat/environment.yml b/modules/nf-core/ascat/environment.yml index 63d87708d6a..c5cfc59e15f 100644 --- a/modules/nf-core/ascat/environment.yml +++ b/modules/nf-core/ascat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ashlar/environment.yml b/modules/nf-core/ashlar/environment.yml index 502f7177299..c80ee158aed 100644 --- a/modules/nf-core/ashlar/environment.yml +++ b/modules/nf-core/ashlar/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/assemblyscan/environment.yml b/modules/nf-core/assemblyscan/environment.yml index 3751ff08a2c..47655d685c1 100644 --- a/modules/nf-core/assemblyscan/environment.yml +++ b/modules/nf-core/assemblyscan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ataqv/ataqv/environment.yml b/modules/nf-core/ataqv/ataqv/environment.yml index 8ad29081b19..0023d8941f1 100644 --- a/modules/nf-core/ataqv/ataqv/environment.yml +++ b/modules/nf-core/ataqv/ataqv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ataqv/mkarv/environment.yml b/modules/nf-core/ataqv/mkarv/environment.yml index 8ad29081b19..0023d8941f1 100644 --- a/modules/nf-core/ataqv/mkarv/environment.yml +++ b/modules/nf-core/ataqv/mkarv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/atlas/call/environment.yml b/modules/nf-core/atlas/call/environment.yml index 51ea2964b5b..8605763db3b 100644 --- a/modules/nf-core/atlas/call/environment.yml +++ b/modules/nf-core/atlas/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/atlas/pmd/environment.yml b/modules/nf-core/atlas/pmd/environment.yml index 51ea2964b5b..8605763db3b 100644 --- a/modules/nf-core/atlas/pmd/environment.yml +++ b/modules/nf-core/atlas/pmd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/atlas/recal/environment.yml b/modules/nf-core/atlas/recal/environment.yml index 51ea2964b5b..8605763db3b 100644 --- a/modules/nf-core/atlas/recal/environment.yml +++ b/modules/nf-core/atlas/recal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/atlas/splitmerge/environment.yml b/modules/nf-core/atlas/splitmerge/environment.yml index 51ea2964b5b..8605763db3b 100644 --- a/modules/nf-core/atlas/splitmerge/environment.yml +++ b/modules/nf-core/atlas/splitmerge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml index 9c0280fc49e..def8c5dfd2b 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/authentict/deam2cont/environment.yml b/modules/nf-core/authentict/deam2cont/environment.yml index 73d01c656e5..a6bbfba4b39 100644 --- a/modules/nf-core/authentict/deam2cont/environment.yml +++ b/modules/nf-core/authentict/deam2cont/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bacphlip/environment.yml b/modules/nf-core/bacphlip/environment.yml index bfd7a480b82..61ea5ad16c1 100644 --- a/modules/nf-core/bacphlip/environment.yml +++ b/modules/nf-core/bacphlip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml index a2d0ff725f1..c1b616a451b 100644 --- a/modules/nf-core/bakta/bakta/environment.yml +++ b/modules/nf-core/bakta/bakta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml index 83a069764d8..c1b616a451b 100644 --- a/modules/nf-core/bakta/baktadbdownload/environment.yml +++ b/modules/nf-core/bakta/baktadbdownload/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bakta=1.10.4 \ No newline at end of file + - bioconda::bakta=1.10.4 diff --git a/modules/nf-core/bam2fastx/bam2fastq/environment.yml b/modules/nf-core/bam2fastx/bam2fastq/environment.yml index 563a0c17b36..684cd2e5f9e 100644 --- a/modules/nf-core/bam2fastx/bam2fastq/environment.yml +++ b/modules/nf-core/bam2fastx/bam2fastq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamaligncleaner/environment.yml b/modules/nf-core/bamaligncleaner/environment.yml index 8b861d9ea88..d25b50388f9 100644 --- a/modules/nf-core/bamaligncleaner/environment.yml +++ b/modules/nf-core/bamaligncleaner/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamclipper/environment.yml b/modules/nf-core/bamclipper/environment.yml index 1d24949aa0f..96ebf5a5394 100644 --- a/modules/nf-core/bamclipper/environment.yml +++ b/modules/nf-core/bamclipper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamcmp/environment.yml b/modules/nf-core/bamcmp/environment.yml index 351c12ab93b..edc63a3adcc 100644 --- a/modules/nf-core/bamcmp/environment.yml +++ b/modules/nf-core/bamcmp/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamstats/generalstats/environment.yml b/modules/nf-core/bamstats/generalstats/environment.yml index 4591b2cc5c5..820a1b9290d 100644 --- a/modules/nf-core/bamstats/generalstats/environment.yml +++ b/modules/nf-core/bamstats/generalstats/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bamstats=0.3.5" + - bioconda::bamstats=0.3.5 diff --git a/modules/nf-core/bamtofastq10x/environment.yml b/modules/nf-core/bamtofastq10x/environment.yml index cce34f4b9bd..0d4ec00c657 100644 --- a/modules/nf-core/bamtofastq10x/environment.yml +++ b/modules/nf-core/bamtofastq10x/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::10x_bamtofastq=1.4.1" + - bioconda::10x_bamtofastq=1.4.1 diff --git a/modules/nf-core/bamtools/convert/environment.yml b/modules/nf-core/bamtools/convert/environment.yml index 5fd41c95be3..5ee33607516 100644 --- a/modules/nf-core/bamtools/convert/environment.yml +++ b/modules/nf-core/bamtools/convert/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamtools/split/environment.yml b/modules/nf-core/bamtools/split/environment.yml index 5fd41c95be3..5ee33607516 100644 --- a/modules/nf-core/bamtools/split/environment.yml +++ b/modules/nf-core/bamtools/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamtools/stats/environment.yml b/modules/nf-core/bamtools/stats/environment.yml index 5fd41c95be3..5ee33607516 100644 --- a/modules/nf-core/bamtools/stats/environment.yml +++ b/modules/nf-core/bamtools/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bamutil/trimbam/environment.yml b/modules/nf-core/bamutil/trimbam/environment.yml index d9ac63d520f..def554ec247 100644 --- a/modules/nf-core/bamutil/trimbam/environment.yml +++ b/modules/nf-core/bamutil/trimbam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bandage/image/environment.yml b/modules/nf-core/bandage/image/environment.yml index 018e544b96b..7a672e39b7a 100644 --- a/modules/nf-core/bandage/image/environment.yml +++ b/modules/nf-core/bandage/image/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/barrnap/environment.yml b/modules/nf-core/barrnap/environment.yml index 3a920f2e3f2..f355fb7b227 100644 --- a/modules/nf-core/barrnap/environment.yml +++ b/modules/nf-core/barrnap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/basicpy/environment.yml b/modules/nf-core/basicpy/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/basicpy/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml index 7ff25c7a51b..977fb4ba4a4 100644 --- a/modules/nf-core/bbmap/align/environment.yml +++ b/modules/nf-core/bbmap/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/bbduk/environment.yml +++ b/modules/nf-core/bbmap/bbduk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/bbmerge/environment.yml b/modules/nf-core/bbmap/bbmerge/environment.yml index 8343bef8092..f76f417a31b 100644 --- a/modules/nf-core/bbmap/bbmerge/environment.yml +++ b/modules/nf-core/bbmap/bbmerge/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bbmap=39.10" + - bioconda::bbmap=39.10 diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml index fa8209c0b54..5dfe793f98e 100644 --- a/modules/nf-core/bbmap/bbnorm/environment.yml +++ b/modules/nf-core/bbmap/bbnorm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/clumpify/environment.yml b/modules/nf-core/bbmap/clumpify/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/clumpify/environment.yml +++ b/modules/nf-core/bbmap/clumpify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/filterbyname/environment.yml b/modules/nf-core/bbmap/filterbyname/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/filterbyname/environment.yml +++ b/modules/nf-core/bbmap/filterbyname/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/index/environment.yml +++ b/modules/nf-core/bbmap/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/pileup/environment.yml b/modules/nf-core/bbmap/pileup/environment.yml index 7ff25c7a51b..977fb4ba4a4 100644 --- a/modules/nf-core/bbmap/pileup/environment.yml +++ b/modules/nf-core/bbmap/pileup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/repair/environment.yml b/modules/nf-core/bbmap/repair/environment.yml index 4e65bfe6a99..b609e090138 100644 --- a/modules/nf-core/bbmap/repair/environment.yml +++ b/modules/nf-core/bbmap/repair/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bbmap=39.13" + - bioconda::bbmap=39.13 diff --git a/modules/nf-core/bbmap/sendsketch/environment.yml b/modules/nf-core/bbmap/sendsketch/environment.yml index a2f65506783..f76f417a31b 100644 --- a/modules/nf-core/bbmap/sendsketch/environment.yml +++ b/modules/nf-core/bbmap/sendsketch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/call/environment.yml b/modules/nf-core/bcftools/call/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/call/environment.yml +++ b/modules/nf-core/bcftools/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/consensus/environment.yml b/modules/nf-core/bcftools/consensus/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/consensus/environment.yml +++ b/modules/nf-core/bcftools/consensus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/convert/environment.yml b/modules/nf-core/bcftools/convert/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/convert/environment.yml +++ b/modules/nf-core/bcftools/convert/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/csq/environment.yml b/modules/nf-core/bcftools/csq/environment.yml index 20fc663a5e3..b276efd90d3 100644 --- a/modules/nf-core/bcftools/csq/environment.yml +++ b/modules/nf-core/bcftools/csq/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bcftools=1.20" + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/index/environment.yml +++ b/modules/nf-core/bcftools/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/isec/environment.yml b/modules/nf-core/bcftools/isec/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/isec/environment.yml +++ b/modules/nf-core/bcftools/isec/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/mpileup/environment.yml +++ b/modules/nf-core/bcftools/mpileup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/pluginimputeinfo/environment.yml b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml index bfd03513359..b276efd90d3 100644 --- a/modules/nf-core/bcftools/pluginimputeinfo/environment.yml +++ b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bcftools=1.20" + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/pluginsetgt/environment.yml b/modules/nf-core/bcftools/pluginsetgt/environment.yml index a394b026327..557488607c7 100644 --- a/modules/nf-core/bcftools/pluginsetgt/environment.yml +++ b/modules/nf-core/bcftools/pluginsetgt/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bcftools=1.21" + - bioconda::bcftools=1.21 diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/pluginsplit/environment.yml +++ b/modules/nf-core/bcftools/pluginsplit/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/plugintag2tag/environment.yml b/modules/nf-core/bcftools/plugintag2tag/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/plugintag2tag/environment.yml +++ b/modules/nf-core/bcftools/plugintag2tag/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/roh/environment.yml b/modules/nf-core/bcftools/roh/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/roh/environment.yml +++ b/modules/nf-core/bcftools/roh/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/split/environment.yml b/modules/nf-core/bcftools/split/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/split/environment.yml +++ b/modules/nf-core/bcftools/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 93357b41ead..a80302fcf68 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml index 5c00b116ad9..b276efd90d3 100644 --- a/modules/nf-core/bcftools/view/environment.yml +++ b/modules/nf-core/bcftools/view/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/beagle5/beagle/environment.yml b/modules/nf-core/beagle5/beagle/environment.yml index 55ed1d1bda3..8cba610d74b 100644 --- a/modules/nf-core/beagle5/beagle/environment.yml +++ b/modules/nf-core/beagle5/beagle/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedgovcf/environment.yml b/modules/nf-core/bedgovcf/environment.yml index 4b32f5201e1..9d2a68fd9a6 100644 --- a/modules/nf-core/bedgovcf/environment.yml +++ b/modules/nf-core/bedgovcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedops/convert2bed/environment.yml b/modules/nf-core/bedops/convert2bed/environment.yml index 3c13066f792..6fd30aaf17d 100644 --- a/modules/nf-core/bedops/convert2bed/environment.yml +++ b/modules/nf-core/bedops/convert2bed/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bedops=2.4.41" + - bioconda::bedops=2.4.41 diff --git a/modules/nf-core/bedops/gtf2bed/environment.yml b/modules/nf-core/bedops/gtf2bed/environment.yml index 3c13066f792..6fd30aaf17d 100644 --- a/modules/nf-core/bedops/gtf2bed/environment.yml +++ b/modules/nf-core/bedops/gtf2bed/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bedops=2.4.41" + - bioconda::bedops=2.4.41 diff --git a/modules/nf-core/bedtools/bamtobed/environment.yml b/modules/nf-core/bedtools/bamtobed/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/bamtobed/environment.yml +++ b/modules/nf-core/bedtools/bamtobed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/closest/environment.yml b/modules/nf-core/bedtools/closest/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/closest/environment.yml +++ b/modules/nf-core/bedtools/closest/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/complement/environment.yml b/modules/nf-core/bedtools/complement/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/complement/environment.yml +++ b/modules/nf-core/bedtools/complement/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/coverage/environment.yml b/modules/nf-core/bedtools/coverage/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/coverage/environment.yml +++ b/modules/nf-core/bedtools/coverage/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/getfasta/environment.yml b/modules/nf-core/bedtools/getfasta/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/getfasta/environment.yml +++ b/modules/nf-core/bedtools/getfasta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/groupby/environment.yml b/modules/nf-core/bedtools/groupby/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/groupby/environment.yml +++ b/modules/nf-core/bedtools/groupby/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/intersect/environment.yml b/modules/nf-core/bedtools/intersect/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/intersect/environment.yml +++ b/modules/nf-core/bedtools/intersect/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/jaccard/environment.yml b/modules/nf-core/bedtools/jaccard/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/jaccard/environment.yml +++ b/modules/nf-core/bedtools/jaccard/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/makewindows/environment.yml b/modules/nf-core/bedtools/makewindows/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/makewindows/environment.yml +++ b/modules/nf-core/bedtools/makewindows/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/map/environment.yml b/modules/nf-core/bedtools/map/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/map/environment.yml +++ b/modules/nf-core/bedtools/map/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/maskfasta/environment.yml b/modules/nf-core/bedtools/maskfasta/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/maskfasta/environment.yml +++ b/modules/nf-core/bedtools/maskfasta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/multiinter/environment.yml b/modules/nf-core/bedtools/multiinter/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/multiinter/environment.yml +++ b/modules/nf-core/bedtools/multiinter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/nuc/environment.yml b/modules/nf-core/bedtools/nuc/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/nuc/environment.yml +++ b/modules/nf-core/bedtools/nuc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/shift/environment.yml b/modules/nf-core/bedtools/shift/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/shift/environment.yml +++ b/modules/nf-core/bedtools/shift/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/slop/environment.yml b/modules/nf-core/bedtools/slop/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/slop/environment.yml +++ b/modules/nf-core/bedtools/slop/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/split/environment.yml b/modules/nf-core/bedtools/split/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/split/environment.yml +++ b/modules/nf-core/bedtools/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/subtract/environment.yml b/modules/nf-core/bedtools/subtract/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/subtract/environment.yml +++ b/modules/nf-core/bedtools/subtract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/unionbedg/environment.yml b/modules/nf-core/bedtools/unionbedg/environment.yml index 5683bc05f23..45c307b0e4f 100644 --- a/modules/nf-core/bedtools/unionbedg/environment.yml +++ b/modules/nf-core/bedtools/unionbedg/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml index 527f6cd4b1c..0be1e105fb0 100644 --- a/modules/nf-core/bioawk/environment.yml +++ b/modules/nf-core/bioawk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biobambam/bammarkduplicates2/environment.yml b/modules/nf-core/biobambam/bammarkduplicates2/environment.yml index eb19895afd0..8c8c3166670 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/environment.yml +++ b/modules/nf-core/biobambam/bammarkduplicates2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biobambam/bammerge/environment.yml b/modules/nf-core/biobambam/bammerge/environment.yml index eb19895afd0..8c8c3166670 100644 --- a/modules/nf-core/biobambam/bammerge/environment.yml +++ b/modules/nf-core/biobambam/bammerge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biobambam/bamsormadup/environment.yml b/modules/nf-core/biobambam/bamsormadup/environment.yml index eb19895afd0..8c8c3166670 100644 --- a/modules/nf-core/biobambam/bamsormadup/environment.yml +++ b/modules/nf-core/biobambam/bamsormadup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biohansel/environment.yml b/modules/nf-core/biohansel/environment.yml index b20be7488bf..37f32dd7e39 100644 --- a/modules/nf-core/biohansel/environment.yml +++ b/modules/nf-core/biohansel/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/align/environment.yml b/modules/nf-core/biscuit/align/environment.yml index 222c156ed9a..c452743b813 100644 --- a/modules/nf-core/biscuit/align/environment.yml +++ b/modules/nf-core/biscuit/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/biscuitblaster/environment.yml b/modules/nf-core/biscuit/biscuitblaster/environment.yml index 74a7b2fb908..6ce87bb04bd 100644 --- a/modules/nf-core/biscuit/biscuitblaster/environment.yml +++ b/modules/nf-core/biscuit/biscuitblaster/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/bsconv/environment.yml b/modules/nf-core/biscuit/bsconv/environment.yml index 123215dc20f..26e418b0dc2 100644 --- a/modules/nf-core/biscuit/bsconv/environment.yml +++ b/modules/nf-core/biscuit/bsconv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/epiread/environment.yml b/modules/nf-core/biscuit/epiread/environment.yml index 222c156ed9a..c452743b813 100644 --- a/modules/nf-core/biscuit/epiread/environment.yml +++ b/modules/nf-core/biscuit/epiread/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/index/environment.yml b/modules/nf-core/biscuit/index/environment.yml index 123215dc20f..26e418b0dc2 100644 --- a/modules/nf-core/biscuit/index/environment.yml +++ b/modules/nf-core/biscuit/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/mergecg/environment.yml b/modules/nf-core/biscuit/mergecg/environment.yml index 222c156ed9a..c452743b813 100644 --- a/modules/nf-core/biscuit/mergecg/environment.yml +++ b/modules/nf-core/biscuit/mergecg/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/pileup/environment.yml b/modules/nf-core/biscuit/pileup/environment.yml index 222c156ed9a..c452743b813 100644 --- a/modules/nf-core/biscuit/pileup/environment.yml +++ b/modules/nf-core/biscuit/pileup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/qc/environment.yml b/modules/nf-core/biscuit/qc/environment.yml index 123215dc20f..26e418b0dc2 100644 --- a/modules/nf-core/biscuit/qc/environment.yml +++ b/modules/nf-core/biscuit/qc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/biscuit/vcf2bed/environment.yml b/modules/nf-core/biscuit/vcf2bed/environment.yml index 222c156ed9a..c452743b813 100644 --- a/modules/nf-core/biscuit/vcf2bed/environment.yml +++ b/modules/nf-core/biscuit/vcf2bed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/align/environment.yml b/modules/nf-core/bismark/align/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/align/environment.yml +++ b/modules/nf-core/bismark/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/coverage2cytosine/environment.yml b/modules/nf-core/bismark/coverage2cytosine/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/coverage2cytosine/environment.yml +++ b/modules/nf-core/bismark/coverage2cytosine/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/deduplicate/environment.yml b/modules/nf-core/bismark/deduplicate/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/deduplicate/environment.yml +++ b/modules/nf-core/bismark/deduplicate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/genomepreparation/environment.yml +++ b/modules/nf-core/bismark/genomepreparation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/methylationextractor/environment.yml b/modules/nf-core/bismark/methylationextractor/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/methylationextractor/environment.yml +++ b/modules/nf-core/bismark/methylationextractor/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/report/environment.yml b/modules/nf-core/bismark/report/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/report/environment.yml +++ b/modules/nf-core/bismark/report/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bismark/summary/environment.yml b/modules/nf-core/bismark/summary/environment.yml index 9bc4753bdab..5f6be275612 100644 --- a/modules/nf-core/bismark/summary/environment.yml +++ b/modules/nf-core/bismark/summary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/blast/blastdbcmd/environment.yml b/modules/nf-core/blast/blastdbcmd/environment.yml index 78ed204d7f9..968930b63d9 100644 --- a/modules/nf-core/blast/blastdbcmd/environment.yml +++ b/modules/nf-core/blast/blastdbcmd/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::blast=2.15.0" + - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/blastn/environment.yml b/modules/nf-core/blast/blastn/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/blast/blastn/environment.yml +++ b/modules/nf-core/blast/blastn/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/blast/blastp/environment.yml b/modules/nf-core/blast/blastp/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/blast/blastp/environment.yml +++ b/modules/nf-core/blast/blastp/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/blast/makeblastdb/environment.yml b/modules/nf-core/blast/makeblastdb/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/blast/makeblastdb/environment.yml +++ b/modules/nf-core/blast/makeblastdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/blast/tblastn/environment.yml b/modules/nf-core/blast/tblastn/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/blast/tblastn/environment.yml +++ b/modules/nf-core/blast/tblastn/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/blast/updateblastdb/environment.yml b/modules/nf-core/blast/updateblastdb/environment.yml index 78ed204d7f9..968930b63d9 100644 --- a/modules/nf-core/blast/updateblastdb/environment.yml +++ b/modules/nf-core/blast/updateblastdb/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::blast=2.15.0" + - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blat/environment.yml b/modules/nf-core/blat/environment.yml index 2a85c07875d..03e1d42248d 100644 --- a/modules/nf-core/blat/environment.yml +++ b/modules/nf-core/blat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index 61bd69c2c7a..40d9b03668f 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -1,8 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/bowtie - - bioconda::bowtie=1.3.1 # renovate: datasource=conda depName=bioconda/samtools + - bioconda::bowtie=1.3.1 + - bioconda::bowtie=1.3.1 - bioconda::samtools=1.20 diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml index 61bd69c2c7a..fff53becc93 100644 --- a/modules/nf-core/bowtie/build/environment.yml +++ b/modules/nf-core/bowtie/build/environment.yml @@ -1,8 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: # renovate: datasource=conda depName=bioconda/bowtie - bioconda::bowtie=1.3.1 - # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.20 diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml index 9090f218834..0be95906754 100644 --- a/modules/nf-core/bowtie2/align/environment.yml +++ b/modules/nf-core/bowtie2/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml index e590f7ce326..e5e95df01af 100644 --- a/modules/nf-core/bowtie2/build/environment.yml +++ b/modules/nf-core/bowtie2/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml index b96b00d7a3b..5730fc9a1cc 100644 --- a/modules/nf-core/bracken/bracken/environment.yml +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bracken=2.9" + - bioconda::bracken=2.9 diff --git a/modules/nf-core/bracken/build/environment.yml b/modules/nf-core/bracken/build/environment.yml index d9ea9a61e52..5730fc9a1cc 100644 --- a/modules/nf-core/bracken/build/environment.yml +++ b/modules/nf-core/bracken/build/environment.yml @@ -1,6 +1,7 @@ --- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bracken=2.9" + - bioconda::bracken=2.9 diff --git a/modules/nf-core/bracken/combinebrackenoutputs/environment.yml b/modules/nf-core/bracken/combinebrackenoutputs/environment.yml index b96b00d7a3b..5730fc9a1cc 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/environment.yml +++ b/modules/nf-core/bracken/combinebrackenoutputs/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bracken=2.9" + - bioconda::bracken=2.9 diff --git a/modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/busco/environment.yml index 53e5e90e394..2c2fa664c83 100644 --- a/modules/nf-core/busco/busco/environment.yml +++ b/modules/nf-core/busco/busco/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/busco/generateplot/environment.yml b/modules/nf-core/busco/generateplot/environment.yml index 53e5e90e394..2c2fa664c83 100644 --- a/modules/nf-core/busco/generateplot/environment.yml +++ b/modules/nf-core/busco/generateplot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/aln/environment.yml b/modules/nf-core/bwa/aln/environment.yml index d8789a20928..35c9da752d2 100644 --- a/modules/nf-core/bwa/aln/environment.yml +++ b/modules/nf-core/bwa/aln/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index d8789a20928..35c9da752d2 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index ef7b966c0fa..b5f4d6952b7 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/sampe/environment.yml b/modules/nf-core/bwa/sampe/environment.yml index 7576715281c..c60bb1b5866 100644 --- a/modules/nf-core/bwa/sampe/environment.yml +++ b/modules/nf-core/bwa/sampe/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwa/samse/environment.yml b/modules/nf-core/bwa/samse/environment.yml index 7576715281c..c60bb1b5866 100644 --- a/modules/nf-core/bwa/samse/environment.yml +++ b/modules/nf-core/bwa/samse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml index 15cee238767..5b4b415a9d5 100644 --- a/modules/nf-core/bwamem2/index/environment.yml +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 7e0b5a34795..03ce36562b3 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwameme/index/environment.yml b/modules/nf-core/bwameme/index/environment.yml index f209d62e86e..631a89868d1 100644 --- a/modules/nf-core/bwameme/index/environment.yml +++ b/modules/nf-core/bwameme/index/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" + - bioconda::bwa-meme=1.0.6 diff --git a/modules/nf-core/bwameme/mem/environment.yml b/modules/nf-core/bwameme/mem/environment.yml index cad7944049a..f0be97b799b 100644 --- a/modules/nf-core/bwameme/mem/environment.yml +++ b/modules/nf-core/bwameme/mem/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" - - "bioconda::mbuffer=20160228" - - "bioconda::samtools=1.20" + - bioconda::bwa-meme=1.0.6 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/bwameth/align/environment.yml b/modules/nf-core/bwameth/align/environment.yml index 707376ebf90..4323fd8f9fe 100644 --- a/modules/nf-core/bwameth/align/environment.yml +++ b/modules/nf-core/bwameth/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bwameth/index/environment.yml b/modules/nf-core/bwameth/index/environment.yml index 707376ebf90..4323fd8f9fe 100644 --- a/modules/nf-core/bwameth/index/environment.yml +++ b/modules/nf-core/bwameth/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml index 4477e16e5b2..d98de652260 100644 --- a/modules/nf-core/cadd/environment.yml +++ b/modules/nf-core/cadd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf index 0af87f6e5b6..9675e2932cd 100644 --- a/modules/nf-core/cadd/main.nf +++ b/modules/nf-core/cadd/main.nf @@ -1,23 +1,23 @@ process CADD { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1' containerOptions { - (workflow.containerEngine == 'singularity') ? - "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" : - "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" - } + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" + : "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" + } input: tuple val(meta), path(vcf) - path(annotation_dir) + path annotation_dir output: tuple val(meta), path("*.tsv.gz"), emit: tsv - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -25,29 +25,31 @@ process CADD { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + def VERSION = "1.6.post1" + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. """ cadd.sh \\ -o ${prefix}.tsv.gz \\ - $args \\ - $vcf + ${args} \\ + ${vcf} cat <<-END_VERSIONS > versions.yml "${task.process}": - cadd: $VERSION + cadd: ${VERSION} END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + def VERSION = "1.6.post1" + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. """ touch ${prefix}.tsv.gz cat <<-END_VERSIONS > versions.yml "${task.process}": - cadd: $VERSION + cadd: ${VERSION} END_VERSIONS """ } diff --git a/modules/nf-core/cafe/environment.yml b/modules/nf-core/cafe/environment.yml index 79c9b6f28fc..774b5dd1864 100644 --- a/modules/nf-core/cafe/environment.yml +++ b/modules/nf-core/cafe/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cafe=5.1.0" + - bioconda::cafe=5.1.0 diff --git a/modules/nf-core/calder2/environment.yml b/modules/nf-core/calder2/environment.yml index 6bbba46df2d..17e4cd31ad0 100644 --- a/modules/nf-core/calder2/environment.yml +++ b/modules/nf-core/calder2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/canu/environment.yml b/modules/nf-core/canu/environment.yml index 9c7f6dd49b1..bb5d0497057 100644 --- a/modules/nf-core/canu/environment.yml +++ b/modules/nf-core/canu/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index 9b01c865a28..50c2059afb1 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/catpack/addnames/environment.yml b/modules/nf-core/catpack/addnames/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/addnames/environment.yml +++ b/modules/nf-core/catpack/addnames/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/bins/environment.yml b/modules/nf-core/catpack/bins/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/bins/environment.yml +++ b/modules/nf-core/catpack/bins/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/contigs/environment.yml b/modules/nf-core/catpack/contigs/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/contigs/environment.yml +++ b/modules/nf-core/catpack/contigs/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/download/environment.yml b/modules/nf-core/catpack/download/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/download/environment.yml +++ b/modules/nf-core/catpack/download/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/prepare/environment.yml b/modules/nf-core/catpack/prepare/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/prepare/environment.yml +++ b/modules/nf-core/catpack/prepare/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/reads/environment.yml b/modules/nf-core/catpack/reads/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/reads/environment.yml +++ b/modules/nf-core/catpack/reads/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/catpack/summarise/environment.yml b/modules/nf-core/catpack/summarise/environment.yml index 20d286ab5b7..39264bf45a1 100644 --- a/modules/nf-core/catpack/summarise/environment.yml +++ b/modules/nf-core/catpack/summarise/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cat=6.0.1" + - bioconda::cat=6.0.1 diff --git a/modules/nf-core/cdhit/cdhit/environment.yml b/modules/nf-core/cdhit/cdhit/environment.yml index 59e671e484c..77894b01c68 100644 --- a/modules/nf-core/cdhit/cdhit/environment.yml +++ b/modules/nf-core/cdhit/cdhit/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cdhit/cdhitest/environment.yml b/modules/nf-core/cdhit/cdhitest/environment.yml index 59e671e484c..77894b01c68 100644 --- a/modules/nf-core/cdhit/cdhitest/environment.yml +++ b/modules/nf-core/cdhit/cdhitest/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cellbender/merge/environment.yml b/modules/nf-core/cellbender/merge/environment.yml index a157c522b2b..3bc6e65c6c7 100644 --- a/modules/nf-core/cellbender/merge/environment.yml +++ b/modules/nf-core/cellbender/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cellbender/removebackground/environment.yml b/modules/nf-core/cellbender/removebackground/environment.yml index d6fb2687868..7b9eceea614 100644 --- a/modules/nf-core/cellbender/removebackground/environment.yml +++ b/modules/nf-core/cellbender/removebackground/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf index f100904f953..0fee6c14b59 100644 --- a/modules/nf-core/cellpose/main.nf +++ b/modules/nf-core/cellpose/main.nf @@ -24,7 +24,6 @@ process CELLPOSE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def model_command = model ? "--pretrained_model $model" : "" - def VERSION = '3.0.1' """ cellpose \\ --image_path $image \\ @@ -34,7 +33,7 @@ process CELLPOSE { cat <<-END_VERSIONS > versions.yml "${task.process}": - cellpose: $VERSION + cellpose: \$(cellpose --version | awk 'NR==2 {print \$3}') END_VERSIONS """ stub: @@ -43,7 +42,6 @@ process CELLPOSE { error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead." } def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "3.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def name = image.name def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name """ @@ -51,7 +49,7 @@ process CELLPOSE { cat <<-END_VERSIONS > versions.yml "${task.process}": - cellpose: $VERSION + cellpose: \$(cellpose --version | awk 'NR==2 {print \$3}') END_VERSIONS """ diff --git a/modules/nf-core/cellrangeratac/count/environment.yml b/modules/nf-core/cellrangeratac/count/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/cellrangeratac/count/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/cellrangeratac/mkfastq/environment.yml b/modules/nf-core/cellrangeratac/mkfastq/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/cellrangeratac/mkfastq/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/cellrangeratac/mkref/environment.yml b/modules/nf-core/cellrangeratac/mkref/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/cellrangeratac/mkref/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/cellsnp/modea/environment.yml b/modules/nf-core/cellsnp/modea/environment.yml index c8b70f595e2..fce6c9fc212 100644 --- a/modules/nf-core/cellsnp/modea/environment.yml +++ b/modules/nf-core/cellsnp/modea/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cellsnp-lite=1.2.3" + - bioconda::cellsnp-lite=1.2.3 diff --git a/modules/nf-core/centrifuge/build/environment.yml b/modules/nf-core/centrifuge/build/environment.yml index b49177e9759..cdfa6489860 100644 --- a/modules/nf-core/centrifuge/build/environment.yml +++ b/modules/nf-core/centrifuge/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml index b49177e9759..cdfa6489860 100644 --- a/modules/nf-core/centrifuge/centrifuge/environment.yml +++ b/modules/nf-core/centrifuge/centrifuge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml index b49177e9759..cdfa6489860 100644 --- a/modules/nf-core/centrifuge/kreport/environment.yml +++ b/modules/nf-core/centrifuge/kreport/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkm/lineagewf/environment.yml b/modules/nf-core/checkm/lineagewf/environment.yml index 1b87050296b..9e854f6b1d3 100644 --- a/modules/nf-core/checkm/lineagewf/environment.yml +++ b/modules/nf-core/checkm/lineagewf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkm/qa/environment.yml b/modules/nf-core/checkm/qa/environment.yml index 1b87050296b..9e854f6b1d3 100644 --- a/modules/nf-core/checkm/qa/environment.yml +++ b/modules/nf-core/checkm/qa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkm2/databasedownload/environment.yml b/modules/nf-core/checkm2/databasedownload/environment.yml index 52d11ba96ba..4536048c73d 100644 --- a/modules/nf-core/checkm2/databasedownload/environment.yml +++ b/modules/nf-core/checkm2/databasedownload/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkm2/predict/environment.yml b/modules/nf-core/checkm2/predict/environment.yml index 18fd1f51a80..0016f7d3b17 100644 --- a/modules/nf-core/checkm2/predict/environment.yml +++ b/modules/nf-core/checkm2/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml index 1a0541303d5..083e17dfd86 100644 --- a/modules/nf-core/checkqc/environment.yml +++ b/modules/nf-core/checkqc/environment.yml @@ -1,10 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - python=3.8 - numpy=1.26 - pip + - python=3.8 - pip: # FIXME https://github.com/nf-core/modules/issues/5814 - checkqc==4.0.3 - interop==1.3.2 diff --git a/modules/nf-core/checkv/downloaddatabase/environment.yml b/modules/nf-core/checkv/downloaddatabase/environment.yml index affce8dddbf..e2eda07ae62 100644 --- a/modules/nf-core/checkv/downloaddatabase/environment.yml +++ b/modules/nf-core/checkv/downloaddatabase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkv/endtoend/environment.yml b/modules/nf-core/checkv/endtoend/environment.yml index affce8dddbf..e2eda07ae62 100644 --- a/modules/nf-core/checkv/endtoend/environment.yml +++ b/modules/nf-core/checkv/endtoend/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/checkv/updatedatabase/environment.yml b/modules/nf-core/checkv/updatedatabase/environment.yml index affce8dddbf..e2eda07ae62 100644 --- a/modules/nf-core/checkv/updatedatabase/environment.yml +++ b/modules/nf-core/checkv/updatedatabase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml index 22fd2e2e842..0b20d94b112 100644 --- a/modules/nf-core/chewbbaca/createschema/environment.yml +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chopper/environment.yml b/modules/nf-core/chopper/environment.yml index 2195b5eda84..ad7348389cf 100644 --- a/modules/nf-core/chopper/environment.yml +++ b/modules/nf-core/chopper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chromap/chromap/environment.yml b/modules/nf-core/chromap/chromap/environment.yml index a59614c03c4..ee8f77a8dd6 100644 --- a/modules/nf-core/chromap/chromap/environment.yml +++ b/modules/nf-core/chromap/chromap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chromap/index/environment.yml b/modules/nf-core/chromap/index/environment.yml index 1eb3f8703d6..af9c7980d95 100644 --- a/modules/nf-core/chromap/index/environment.yml +++ b/modules/nf-core/chromap/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chromograph/environment.yml b/modules/nf-core/chromograph/environment.yml index 47881b1fb6f..cc931c7673b 100644 --- a/modules/nf-core/chromograph/environment.yml +++ b/modules/nf-core/chromograph/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/circexplorer2/annotate/environment.yml b/modules/nf-core/circexplorer2/annotate/environment.yml index c703b088a04..1eac75ec881 100644 --- a/modules/nf-core/circexplorer2/annotate/environment.yml +++ b/modules/nf-core/circexplorer2/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/circexplorer2/parse/environment.yml b/modules/nf-core/circexplorer2/parse/environment.yml index c703b088a04..1eac75ec881 100644 --- a/modules/nf-core/circexplorer2/parse/environment.yml +++ b/modules/nf-core/circexplorer2/parse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/circularmapper/circulargenerator/environment.yml b/modules/nf-core/circularmapper/circulargenerator/environment.yml index 39e62b9baac..b0952b1320a 100644 --- a/modules/nf-core/circularmapper/circulargenerator/environment.yml +++ b/modules/nf-core/circularmapper/circulargenerator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: diff --git a/modules/nf-core/circularmapper/realignsamfile/environment.yml b/modules/nf-core/circularmapper/realignsamfile/environment.yml index ad2c5988126..ae4da3c5222 100644 --- a/modules/nf-core/circularmapper/realignsamfile/environment.yml +++ b/modules/nf-core/circularmapper/realignsamfile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/clame/environment.yml b/modules/nf-core/clame/environment.yml index 4a4f0722745..f93ea7f5a27 100644 --- a/modules/nf-core/clame/environment.yml +++ b/modules/nf-core/clame/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/clipkit/environment.yml b/modules/nf-core/clipkit/environment.yml index 65c451ffb1f..2682ba32733 100644 --- a/modules/nf-core/clipkit/environment.yml +++ b/modules/nf-core/clipkit/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::clipkit=2.3.0" + - bioconda::clipkit=2.3.0 diff --git a/modules/nf-core/clippy/environment.yml b/modules/nf-core/clippy/environment.yml index 4fe9b8860ce..0e937ce43f2 100644 --- a/modules/nf-core/clippy/environment.yml +++ b/modules/nf-core/clippy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/clonalframeml/environment.yml b/modules/nf-core/clonalframeml/environment.yml index f6e2a73cdf8..ad42f73a323 100644 --- a/modules/nf-core/clonalframeml/environment.yml +++ b/modules/nf-core/clonalframeml/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/clustalo/align/environment.yml b/modules/nf-core/clustalo/align/environment.yml index 80bc6a5ad2f..c06768f0d42 100644 --- a/modules/nf-core/clustalo/align/environment.yml +++ b/modules/nf-core/clustalo/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/clustalo/guidetree/environment.yml b/modules/nf-core/clustalo/guidetree/environment.yml index ef4d67285cd..671075e04e0 100644 --- a/modules/nf-core/clustalo/guidetree/environment.yml +++ b/modules/nf-core/clustalo/guidetree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cmseq/polymut/environment.yml b/modules/nf-core/cmseq/polymut/environment.yml index d4417bb1904..fffcd96cce8 100644 --- a/modules/nf-core/cmseq/polymut/environment.yml +++ b/modules/nf-core/cmseq/polymut/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/access/environment.yml b/modules/nf-core/cnvkit/access/environment.yml index 152af54d19d..690d8fd7f77 100644 --- a/modules/nf-core/cnvkit/access/environment.yml +++ b/modules/nf-core/cnvkit/access/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/antitarget/environment.yml b/modules/nf-core/cnvkit/antitarget/environment.yml index b683406cc53..9b3082be065 100644 --- a/modules/nf-core/cnvkit/antitarget/environment.yml +++ b/modules/nf-core/cnvkit/antitarget/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml index 5d793601194..a2466da99f6 100644 --- a/modules/nf-core/cnvkit/batch/environment.yml +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -1,8 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::cnvkit=0.9.10 - - bioconda::htslib=1.17 # Matched with the container - - bioconda::samtools=1.17 # Matched with the container + - bioconda::htslib=1.17 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/cnvkit/call/environment.yml b/modules/nf-core/cnvkit/call/environment.yml index 152af54d19d..690d8fd7f77 100644 --- a/modules/nf-core/cnvkit/call/environment.yml +++ b/modules/nf-core/cnvkit/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/export/environment.yml b/modules/nf-core/cnvkit/export/environment.yml index 152af54d19d..690d8fd7f77 100644 --- a/modules/nf-core/cnvkit/export/environment.yml +++ b/modules/nf-core/cnvkit/export/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/genemetrics/environment.yml b/modules/nf-core/cnvkit/genemetrics/environment.yml index 152af54d19d..690d8fd7f77 100644 --- a/modules/nf-core/cnvkit/genemetrics/environment.yml +++ b/modules/nf-core/cnvkit/genemetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/reference/environment.yml b/modules/nf-core/cnvkit/reference/environment.yml index b683406cc53..9b3082be065 100644 --- a/modules/nf-core/cnvkit/reference/environment.yml +++ b/modules/nf-core/cnvkit/reference/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/target/environment.yml b/modules/nf-core/cnvkit/target/environment.yml index 152af54d19d..690d8fd7f77 100644 --- a/modules/nf-core/cnvkit/target/environment.yml +++ b/modules/nf-core/cnvkit/target/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvnator/cnvnator/environment.yml b/modules/nf-core/cnvnator/cnvnator/environment.yml index 9cd8ebf353e..6f421c9ccae 100644 --- a/modules/nf-core/cnvnator/cnvnator/environment.yml +++ b/modules/nf-core/cnvnator/cnvnator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvnator/convert2vcf/environment.yml b/modules/nf-core/cnvnator/convert2vcf/environment.yml index 9cd8ebf353e..6f421c9ccae 100644 --- a/modules/nf-core/cnvnator/convert2vcf/environment.yml +++ b/modules/nf-core/cnvnator/convert2vcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvpytor/callcnvs/environment.yml b/modules/nf-core/cnvpytor/callcnvs/environment.yml index e66cc1fc8e3..2c7922ff126 100644 --- a/modules/nf-core/cnvpytor/callcnvs/environment.yml +++ b/modules/nf-core/cnvpytor/callcnvs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvpytor/histogram/environment.yml b/modules/nf-core/cnvpytor/histogram/environment.yml index e66cc1fc8e3..2c7922ff126 100644 --- a/modules/nf-core/cnvpytor/histogram/environment.yml +++ b/modules/nf-core/cnvpytor/histogram/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvpytor/importreaddepth/environment.yml b/modules/nf-core/cnvpytor/importreaddepth/environment.yml index cff5d1cd6f0..abf3155006b 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/environment.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::cnvpytor=1.3.1 - - conda-forge::numpy=1.24.3 # Locked from container + - conda-forge::numpy=1.24.3 diff --git a/modules/nf-core/cnvpytor/partition/environment.yml b/modules/nf-core/cnvpytor/partition/environment.yml index e66cc1fc8e3..2c7922ff126 100644 --- a/modules/nf-core/cnvpytor/partition/environment.yml +++ b/modules/nf-core/cnvpytor/partition/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvpytor/view/environment.yml b/modules/nf-core/cnvpytor/view/environment.yml index e66cc1fc8e3..2c7922ff126 100644 --- a/modules/nf-core/cnvpytor/view/environment.yml +++ b/modules/nf-core/cnvpytor/view/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cobrameta/environment.yml b/modules/nf-core/cobrameta/environment.yml index 6e473af8d40..c6634646f70 100644 --- a/modules/nf-core/cobrameta/environment.yml +++ b/modules/nf-core/cobrameta/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::cobra-meta=1.2.3" + - bioconda::cobra-meta=1.2.3 diff --git a/modules/nf-core/cobs/classicconstruct/environment.yml b/modules/nf-core/cobs/classicconstruct/environment.yml index d1f296a1c0d..339ff48f858 100644 --- a/modules/nf-core/cobs/classicconstruct/environment.yml +++ b/modules/nf-core/cobs/classicconstruct/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cobs=0.3.0" + - bioconda::cobs=0.3.0 diff --git a/modules/nf-core/cobs/compactconstruct/environment.yml b/modules/nf-core/cobs/compactconstruct/environment.yml index d1f296a1c0d..339ff48f858 100644 --- a/modules/nf-core/cobs/compactconstruct/environment.yml +++ b/modules/nf-core/cobs/compactconstruct/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::cobs=0.3.0" + - bioconda::cobs=0.3.0 diff --git a/modules/nf-core/concoct/concoct/environment.yml b/modules/nf-core/concoct/concoct/environment.yml index 7db6566e476..2bd60576c04 100644 --- a/modules/nf-core/concoct/concoct/environment.yml +++ b/modules/nf-core/concoct/concoct/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/concoct/concoctcoveragetable/environment.yml b/modules/nf-core/concoct/concoctcoveragetable/environment.yml index 7db6566e476..2bd60576c04 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/environment.yml +++ b/modules/nf-core/concoct/concoctcoveragetable/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/concoct/cutupfasta/environment.yml b/modules/nf-core/concoct/cutupfasta/environment.yml index 7db6566e476..2bd60576c04 100644 --- a/modules/nf-core/concoct/cutupfasta/environment.yml +++ b/modules/nf-core/concoct/cutupfasta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/concoct/extractfastabins/environment.yml b/modules/nf-core/concoct/extractfastabins/environment.yml index 7db6566e476..2bd60576c04 100644 --- a/modules/nf-core/concoct/extractfastabins/environment.yml +++ b/modules/nf-core/concoct/extractfastabins/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/concoct/mergecutupclustering/environment.yml b/modules/nf-core/concoct/mergecutupclustering/environment.yml index 7db6566e476..2bd60576c04 100644 --- a/modules/nf-core/concoct/mergecutupclustering/environment.yml +++ b/modules/nf-core/concoct/mergecutupclustering/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/conifer/environment.yml b/modules/nf-core/conifer/environment.yml index 387668d754f..92ffd984efe 100644 --- a/modules/nf-core/conifer/environment.yml +++ b/modules/nf-core/conifer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/assesssignificance/environment.yml b/modules/nf-core/controlfreec/assesssignificance/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/assesssignificance/environment.yml +++ b/modules/nf-core/controlfreec/assesssignificance/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec/environment.yml b/modules/nf-core/controlfreec/freec/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/freec/environment.yml +++ b/modules/nf-core/controlfreec/freec/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec2bed/environment.yml b/modules/nf-core/controlfreec/freec2bed/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/freec2bed/environment.yml +++ b/modules/nf-core/controlfreec/freec2bed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/freec2circos/environment.yml b/modules/nf-core/controlfreec/freec2circos/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/freec2circos/environment.yml +++ b/modules/nf-core/controlfreec/freec2circos/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/makegraph/environment.yml +++ b/modules/nf-core/controlfreec/makegraph/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/controlfreec/makegraph2/environment.yml b/modules/nf-core/controlfreec/makegraph2/environment.yml index f6b64529bce..3aebc4bde12 100644 --- a/modules/nf-core/controlfreec/makegraph2/environment.yml +++ b/modules/nf-core/controlfreec/makegraph2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/balance/environment.yml b/modules/nf-core/cooler/balance/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/balance/environment.yml +++ b/modules/nf-core/cooler/balance/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/cload/environment.yml b/modules/nf-core/cooler/cload/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/cload/environment.yml +++ b/modules/nf-core/cooler/cload/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/digest/environment.yml b/modules/nf-core/cooler/digest/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/digest/environment.yml +++ b/modules/nf-core/cooler/digest/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/dump/environment.yml b/modules/nf-core/cooler/dump/environment.yml index 45f3b64be0c..bff60eecd1b 100644 --- a/modules/nf-core/cooler/dump/environment.yml +++ b/modules/nf-core/cooler/dump/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/makebins/environment.yml b/modules/nf-core/cooler/makebins/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/makebins/environment.yml +++ b/modules/nf-core/cooler/makebins/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/merge/environment.yml b/modules/nf-core/cooler/merge/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/merge/environment.yml +++ b/modules/nf-core/cooler/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cooler/zoomify/environment.yml b/modules/nf-core/cooler/zoomify/environment.yml index f8165ca96f0..e32bd3ff699 100644 --- a/modules/nf-core/cooler/zoomify/environment.yml +++ b/modules/nf-core/cooler/zoomify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/coptr/estimate/environment.yml b/modules/nf-core/coptr/estimate/environment.yml index c5a150067f6..99bd27824f2 100644 --- a/modules/nf-core/coptr/estimate/environment.yml +++ b/modules/nf-core/coptr/estimate/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coptr=1.1.4" + - bioconda::coptr=1.1.4 diff --git a/modules/nf-core/coptr/extract/environment.yml b/modules/nf-core/coptr/extract/environment.yml index c5a150067f6..99bd27824f2 100644 --- a/modules/nf-core/coptr/extract/environment.yml +++ b/modules/nf-core/coptr/extract/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coptr=1.1.4" + - bioconda::coptr=1.1.4 diff --git a/modules/nf-core/coptr/extract/meta.yml b/modules/nf-core/coptr/extract/meta.yml index 753bc041f1b..efcf71832b9 100644 --- a/modules/nf-core/coptr/extract/meta.yml +++ b/modules/nf-core/coptr/extract/meta.yml @@ -28,7 +28,7 @@ input: description: bam file with the mapping of the reads on the reference genome pattern: "*.{.bam}" ontologies: - - edam: "http://edamontology.org/format_2572" + - edam: "http://edamontology.org/format_2572" output: - coverage: diff --git a/modules/nf-core/coptr/index/environment.yml b/modules/nf-core/coptr/index/environment.yml index c5a150067f6..99bd27824f2 100644 --- a/modules/nf-core/coptr/index/environment.yml +++ b/modules/nf-core/coptr/index/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coptr=1.1.4" + - bioconda::coptr=1.1.4 diff --git a/modules/nf-core/coptr/map/environment.yml b/modules/nf-core/coptr/map/environment.yml index c5a150067f6..99bd27824f2 100644 --- a/modules/nf-core/coptr/map/environment.yml +++ b/modules/nf-core/coptr/map/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coptr=1.1.4" + - bioconda::coptr=1.1.4 diff --git a/modules/nf-core/coptr/merge/environment.yml b/modules/nf-core/coptr/merge/environment.yml index c5a150067f6..99bd27824f2 100644 --- a/modules/nf-core/coptr/merge/environment.yml +++ b/modules/nf-core/coptr/merge/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coptr=1.1.4" + - bioconda::coptr=1.1.4 diff --git a/modules/nf-core/coverm/contig/environment.yml b/modules/nf-core/coverm/contig/environment.yml index eb4b2a44cf3..33e9e6cda22 100644 --- a/modules/nf-core/coverm/contig/environment.yml +++ b/modules/nf-core/coverm/contig/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::coverm=0.7.0" + - bioconda::coverm=0.7.0 diff --git a/modules/nf-core/crisprcleanr/normalize/environment.yml b/modules/nf-core/crisprcleanr/normalize/environment.yml index 7bd19960033..3f6934761eb 100644 --- a/modules/nf-core/crisprcleanr/normalize/environment.yml +++ b/modules/nf-core/crisprcleanr/normalize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/crumble/environment.yml b/modules/nf-core/crumble/environment.yml index 80d35678bfa..1ab560a9882 100644 --- a/modules/nf-core/crumble/environment.yml +++ b/modules/nf-core/crumble/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/csvtk/concat/environment.yml b/modules/nf-core/csvtk/concat/environment.yml index 12087bebfb8..081c81ca131 100644 --- a/modules/nf-core/csvtk/concat/environment.yml +++ b/modules/nf-core/csvtk/concat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml index 12087bebfb8..081c81ca131 100644 --- a/modules/nf-core/csvtk/join/environment.yml +++ b/modules/nf-core/csvtk/join/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/csvtk/split/environment.yml b/modules/nf-core/csvtk/split/environment.yml index 12087bebfb8..081c81ca131 100644 --- a/modules/nf-core/csvtk/split/environment.yml +++ b/modules/nf-core/csvtk/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 9d79af93928..70ee54e328c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/filterdifferentialtable/environment.yml b/modules/nf-core/custom/filterdifferentialtable/environment.yml index b305d6741f5..e998910ef89 100644 --- a/modules/nf-core/custom/filterdifferentialtable/environment.yml +++ b/modules/nf-core/custom/filterdifferentialtable/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2bcd47ee161..9eac2f1e219 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/gtffilter/environment.yml b/modules/nf-core/custom/gtffilter/environment.yml index 800eff9bce1..1d80d11a940 100644 --- a/modules/nf-core/custom/gtffilter/environment.yml +++ b/modules/nf-core/custom/gtffilter/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "conda-forge::python=3.9.5" + - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/matrixfilter/environment.yml b/modules/nf-core/custom/matrixfilter/environment.yml index fb4ebfaa36e..e02bbaefd52 100644 --- a/modules/nf-core/custom/matrixfilter/environment.yml +++ b/modules/nf-core/custom/matrixfilter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml index cd4c3fbe011..4fba538dc4d 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/environment.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml index 2938a35dc84..71def424494 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml @@ -14,7 +14,10 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] - identifier: "" +input: + - - ids: + type: string + description: List of id settings output: - ncbi_settings: - "*.mkfg": diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config index df5def04a0d..3c9471c5727 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config @@ -6,9 +6,9 @@ env.NCBI_SETTINGS = params.settings_file process { withName: CUSTOM_SRATOOLSNCBISETTINGS { containerOptions = { - (workflow.containerEngine == 'singularity') ? - "-B ${params.settings_path}:${params.settings_path}" : - "-v ${params.settings_path}:${params.settings_path}" + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? "-B ${params.settings_path}:${params.settings_path}" + : "-v ${params.settings_path}:${params.settings_path}" } } -} \ No newline at end of file +} diff --git a/modules/nf-core/custom/tabulartogseachip/environment.yml b/modules/nf-core/custom/tabulartogseachip/environment.yml index cc49deffd16..e089d155429 100644 --- a/modules/nf-core/custom/tabulartogseachip/environment.yml +++ b/modules/nf-core/custom/tabulartogseachip/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "conda-forge::gawk=5.1.0" + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/custom/tabulartogseacls/environment.yml +++ b/modules/nf-core/custom/tabulartogseacls/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/custom/tabulartogseagct/environment.yml +++ b/modules/nf-core/custom/tabulartogseagct/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cutadapt/environment.yml b/modules/nf-core/cutadapt/environment.yml index dfdbd1c2a8e..110c0a5e004 100644 --- a/modules/nf-core/cutadapt/environment.yml +++ b/modules/nf-core/cutadapt/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cutesv/environment.yml b/modules/nf-core/cutesv/environment.yml index 4d17f4eda5f..3aa487f904f 100644 --- a/modules/nf-core/cutesv/environment.yml +++ b/modules/nf-core/cutesv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/damageprofiler/environment.yml b/modules/nf-core/damageprofiler/environment.yml index 83cbf093414..a7c3c9c71d8 100644 --- a/modules/nf-core/damageprofiler/environment.yml +++ b/modules/nf-core/damageprofiler/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dastool/dastool/environment.yml b/modules/nf-core/dastool/dastool/environment.yml index 48ee9e0c5ab..23697e2bc6a 100644 --- a/modules/nf-core/dastool/dastool/environment.yml +++ b/modules/nf-core/dastool/dastool/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dastool/fastatocontig2bin/environment.yml b/modules/nf-core/dastool/fastatocontig2bin/environment.yml index 48ee9e0c5ab..23697e2bc6a 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/environment.yml +++ b/modules/nf-core/dastool/fastatocontig2bin/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dastool/scaffolds2bin/environment.yml b/modules/nf-core/dastool/scaffolds2bin/environment.yml index 507ee795b47..2bae7ddd0fe 100644 --- a/modules/nf-core/dastool/scaffolds2bin/environment.yml +++ b/modules/nf-core/dastool/scaffolds2bin/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/datavzrd/environment.yml b/modules/nf-core/datavzrd/environment.yml index 06593466ffa..8b275ebe859 100644 --- a/modules/nf-core/datavzrd/environment.yml +++ b/modules/nf-core/datavzrd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dedup/environment.yml b/modules/nf-core/dedup/environment.yml index 66c1b235d3f..a5d6d9d9b16 100644 --- a/modules/nf-core/dedup/environment.yml +++ b/modules/nf-core/dedup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeparg/downloaddata/environment.yml b/modules/nf-core/deeparg/downloaddata/environment.yml index 074c6501fcb..91c8f5cfca0 100644 --- a/modules/nf-core/deeparg/downloaddata/environment.yml +++ b/modules/nf-core/deeparg/downloaddata/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf index 787c0027968..7f17ebab890 100644 --- a/modules/nf-core/deeparg/downloaddata/main.nf +++ b/modules/nf-core/deeparg/downloaddata/main.nf @@ -2,32 +2,33 @@ process DEEPARG_DOWNLOADDATA { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' : - 'biocontainers/deeparg:1.0.4--pyhdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' + : 'biocontainers/deeparg:1.0.4--pyhdfd78af_0'}" /* We have to force docker/singularity to mount a fake file to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ containerOptions { - "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : - "${workflow.containerEngine}" == 'docker' ? '-v $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : - '' + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' + : "${workflow.containerEngine}" == 'docker' + ? '-v $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' + : '' } - input: - output: - path "db/" , emit: db - path "versions.yml" , emit: versions + path "db/", emit: db + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.4' + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ # Theano needs a writable space and uses the home directory by default, @@ -38,24 +39,30 @@ process DEEPARG_DOWNLOADDATA { deeparg \\ download_data \\ - $args \\ + ${args} \\ -o db/ cat <<-END_VERSIONS > versions.yml "${task.process}": - deeparg: $VERSION + deeparg: ${VERSION} END_VERSIONS """ stub: def args = task.ext.args ?: '' - def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.4' + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ + echo "deeparg \\ + download_data \\ + ${args} \\ + -o db/" + mkdir db/ cat <<-END_VERSIONS > versions.yml "${task.process}": - deeparg: $VERSION + deeparg: ${VERSION} END_VERSIONS """ } diff --git a/modules/nf-core/deeparg/predict/environment.yml b/modules/nf-core/deeparg/predict/environment.yml index 074c6501fcb..91c8f5cfca0 100644 --- a/modules/nf-core/deeparg/predict/environment.yml +++ b/modules/nf-core/deeparg/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeparg/predict/main.nf b/modules/nf-core/deeparg/predict/main.nf index 20fd0a937b0..2ac258a87d3 100644 --- a/modules/nf-core/deeparg/predict/main.nf +++ b/modules/nf-core/deeparg/predict/main.nf @@ -1,32 +1,34 @@ process DEEPARG_PREDICT { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' : - 'biocontainers/deeparg:1.0.4--pyhdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/deeparg:1.0.4--pyhdfd78af_0' + : 'biocontainers/deeparg:1.0.4--pyhdfd78af_0'}" /* We have to force docker/singularity to mount a fake file to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos). Original report: https://github.com/nf-core/funcscan/issues/23 */ containerOptions { - "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : - "${workflow.containerEngine}" == 'docker' ? '-v $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : - '' + ['singularity', 'apptainer'].contains(workflow.containerEngine) + ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' + : "${workflow.containerEngine}" == 'docker' + ? '-v $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' + : '' } input: tuple val(meta), path(fasta), val(model) - path(db) + path db output: - tuple val(meta), path("*.align.daa") , emit: daa - tuple val(meta), path("*.align.daa.tsv") , emit: daa_tsv - tuple val(meta), path("*.mapping.ARG") , emit: arg + tuple val(meta), path("*.align.daa"), emit: daa + tuple val(meta), path("*.align.daa.tsv"), emit: daa_tsv + tuple val(meta), path("*.mapping.ARG"), emit: arg tuple val(meta), path("*.mapping.potential.ARG"), emit: potential_arg - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -34,9 +36,10 @@ process DEEPARG_PREDICT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.4' + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ - DATABASE=`find -L $db -type d -name "database" | sed 's/database//'` + DATABASE=`find -L ${db} -type d -name "database" | sed 's/database//'` # Theano needs a writable space and uses the home directory by default, # but the latter is not always writable, for instance when Singularity @@ -46,22 +49,23 @@ process DEEPARG_PREDICT { deeparg \\ predict \\ - $args \\ - -i $fasta \\ + ${args} \\ + -i ${fasta} \\ -o ${prefix} \\ -d \$DATABASE \\ - --model $model + --model ${model} cat <<-END_VERSIONS > versions.yml "${task.process}": - deeparg: $VERSION + deeparg: ${VERSION} END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION='1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.0.4' + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.align.daa touch ${prefix}.align.daa.tsv @@ -70,7 +74,7 @@ process DEEPARG_PREDICT { cat <<-END_VERSIONS > versions.yml "${task.process}": - deeparg: $VERSION + deeparg: ${VERSION} END_VERSIONS """ } diff --git a/modules/nf-core/deepbgc/download/environment.yml b/modules/nf-core/deepbgc/download/environment.yml index 36cb903fa63..999c6864fe4 100644 --- a/modules/nf-core/deepbgc/download/environment.yml +++ b/modules/nf-core/deepbgc/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deepbgc/pipeline/environment.yml b/modules/nf-core/deepbgc/pipeline/environment.yml index 36cb903fa63..999c6864fe4 100644 --- a/modules/nf-core/deepbgc/pipeline/environment.yml +++ b/modules/nf-core/deepbgc/pipeline/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeptmhmm/environment.yml b/modules/nf-core/deeptmhmm/environment.yml index b4bc7415a68..8a7ea748826 100644 --- a/modules/nf-core/deeptmhmm/environment.yml +++ b/modules/nf-core/deeptmhmm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeptools/alignmentsieve/environment.yml b/modules/nf-core/deeptools/alignmentsieve/environment.yml index d8e208ca830..40bec9452ad 100644 --- a/modules/nf-core/deeptools/alignmentsieve/environment.yml +++ b/modules/nf-core/deeptools/alignmentsieve/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeptools/bamcoverage/environment.yml b/modules/nf-core/deeptools/bamcoverage/environment.yml index d8e208ca830..40bec9452ad 100644 --- a/modules/nf-core/deeptools/bamcoverage/environment.yml +++ b/modules/nf-core/deeptools/bamcoverage/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/deeptools/computematrix/environment.yml b/modules/nf-core/deeptools/computematrix/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/computematrix/environment.yml +++ b/modules/nf-core/deeptools/computematrix/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/multibamsummary/environment.yml b/modules/nf-core/deeptools/multibamsummary/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/multibamsummary/environment.yml +++ b/modules/nf-core/deeptools/multibamsummary/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/plotcorrelation/environment.yml b/modules/nf-core/deeptools/plotcorrelation/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/plotcorrelation/environment.yml +++ b/modules/nf-core/deeptools/plotcorrelation/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/plotfingerprint/environment.yml b/modules/nf-core/deeptools/plotfingerprint/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/plotfingerprint/environment.yml +++ b/modules/nf-core/deeptools/plotfingerprint/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/plotheatmap/environment.yml b/modules/nf-core/deeptools/plotheatmap/environment.yml index 72135bc4c75..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/plotheatmap/environment.yml +++ b/modules/nf-core/deeptools/plotheatmap/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/plotpca/environment.yml b/modules/nf-core/deeptools/plotpca/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/plotpca/environment.yml +++ b/modules/nf-core/deeptools/plotpca/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/deeptools/plotprofile/environment.yml b/modules/nf-core/deeptools/plotprofile/environment.yml index 8880b9b6d2e..0c80282ff2e 100644 --- a/modules/nf-core/deeptools/plotprofile/environment.yml +++ b/modules/nf-core/deeptools/plotprofile/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::deeptools=3.5.5" + - bioconda::deeptools=3.5.5 diff --git a/modules/nf-core/delly/call/environment.yml b/modules/nf-core/delly/call/environment.yml index 5598247e1ae..2b0c93ccce2 100644 --- a/modules/nf-core/delly/call/environment.yml +++ b/modules/nf-core/delly/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/demuxem/environment.yml b/modules/nf-core/demuxem/environment.yml index c74f84be28b..db39832a34a 100644 --- a/modules/nf-core/demuxem/environment.yml +++ b/modules/nf-core/demuxem/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::demuxem=0.1.7.post1" + - bioconda::demuxem=0.1.7.post1 diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml index 4f0b1d103a3..4070836817b 100644 --- a/modules/nf-core/deseq2/differential/environment.yml +++ b/modules/nf-core/deseq2/differential/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/diamond/blastp/environment.yml b/modules/nf-core/diamond/blastp/environment.yml index 950c3c5c55e..6a9b16a2dcf 100644 --- a/modules/nf-core/diamond/blastp/environment.yml +++ b/modules/nf-core/diamond/blastp/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::diamond=2.1.8 + - bioconda::diamond=2.1.11 diff --git a/modules/nf-core/diamond/blastp/main.nf b/modules/nf-core/diamond/blastp/main.nf index dc01cdcc08c..6dd8d3925ad 100644 --- a/modules/nf-core/diamond/blastp/main.nf +++ b/modules/nf-core/diamond/blastp/main.nf @@ -1,27 +1,27 @@ process DIAMOND_BLASTP { tag "$meta.id" - label 'process_medium' + label 'process_high' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/diamond:2.1.8--h43eeafb_0' : - 'biocontainers/diamond:2.1.8--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/diamond:2.1.11--h5ca1c30_0' : + 'biocontainers/diamond:2.1.11--h5ca1c30_0' }" input: tuple val(meta) , path(fasta) tuple val(meta2), path(db) - val out_ext + val outfmt val blast_columns output: - tuple val(meta), path('*.blast'), optional: true, emit: blast - tuple val(meta), path('*.xml') , optional: true, emit: xml - tuple val(meta), path('*.txt') , optional: true, emit: txt - tuple val(meta), path('*.daa') , optional: true, emit: daa - tuple val(meta), path('*.sam') , optional: true, emit: sam - tuple val(meta), path('*.tsv') , optional: true, emit: tsv - tuple val(meta), path('*.paf') , optional: true, emit: paf - path "versions.yml" , emit: versions + tuple val(meta), path('*.{blast,blast.gz}'), optional: true, emit: blast + tuple val(meta), path('*.{xml,xml.gz}') , optional: true, emit: xml + tuple val(meta), path('*.{txt,txt.gz}') , optional: true, emit: txt + tuple val(meta), path('*.{daa,daa.gz}') , optional: true, emit: daa + tuple val(meta), path('*.{sam,sam.gz}') , optional: true, emit: sam + tuple val(meta), path('*.{tsv,tsv.gz}') , optional: true, emit: tsv + tuple val(meta), path('*.{paf,paf.gz}') , optional: true, emit: paf + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -29,35 +29,38 @@ process DIAMOND_BLASTP { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def is_compressed = fasta.getExtension() == "gz" ? true : false - def fasta_name = is_compressed ? fasta.getBaseName() : fasta + def columns = blast_columns ? "${blast_columns}" : '' - switch ( out_ext ) { - case "blast": outfmt = 0; break - case "xml": outfmt = 5; break - case "txt": outfmt = 6; break - case "daa": outfmt = 100; break - case "sam": outfmt = 101; break - case "tsv": outfmt = 102; break - case "paf": outfmt = 103; break - default: - outfmt = '6'; - out_ext = 'txt'; - log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)"); - break + def out_ext = "" + + if (outfmt == 0) { + out_ext = "blast" + } else if (outfmt == 5) { + out_ext = "xml" + } else if (outfmt == 6) { + out_ext = "txt" + } else if (outfmt == 100) { + out_ext = "daa" + } else if (outfmt == 101) { + out_ext = "sam" + } else if (outfmt == 102) { + out_ext = "tsv" + } else if (outfmt == 103) { + out_ext = "paf" + } else { + log.warn("Unknown output file format provided (${outfmt}): selecting DIAMOND default of tabular BLAST output (txt)") + outfmt = 6 + out_ext = 'txt' } - """ - if [ "${is_compressed}" == "true" ]; then - gzip -c -d ${fasta} > ${fasta_name} - fi - DB=`find -L ./ -name "*.dmnd" | sed 's/\\.dmnd\$//'` + if ( args =~ /--compress\s+1/ ) out_ext += '.gz' + """ diamond \\ blastp \\ --threads ${task.cpus} \\ - --db \$DB \\ - --query ${fasta_name} \\ + --db ${db} \\ + --query ${fasta} \\ --outfmt ${outfmt} ${columns} \\ ${args} \\ --out ${prefix}.${out_ext} @@ -69,23 +72,32 @@ process DIAMOND_BLASTP { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - switch ( out_ext ) { - case "blast": outfmt = 0; break - case "xml": outfmt = 5; break - case "txt": outfmt = 6; break - case "daa": outfmt = 100; break - case "sam": outfmt = 101; break - case "tsv": outfmt = 102; break - case "paf": outfmt = 103; break - default: - outfmt = '6'; - out_ext = 'txt'; - log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)"); - break + + def out_ext = "" + + if (outfmt == 0) { + out_ext = "blast" + } else if (outfmt == 5) { + out_ext = "xml" + } else if (outfmt == 6) { + out_ext = "txt" + } else if (outfmt == 100) { + out_ext = "daa" + } else if (outfmt == 101) { + out_ext = "sam" + } else if (outfmt == 102) { + out_ext = "tsv" + } else if (outfmt == 103) { + out_ext = "paf" + } else { + log.warn("Unknown output file format provided (${outfmt}): selecting DIAMOND default of tabular BLAST output (txt)") + outfmt = 6 + out_ext = 'txt' } + if ( args =~ /--compress\s+1/ ) out_ext += '.gz' + """ touch ${prefix}.${out_ext} diff --git a/modules/nf-core/diamond/blastp/meta.yml b/modules/nf-core/diamond/blastp/meta.yml index fbddfbd00f1..6518aa9aedd 100644 --- a/modules/nf-core/diamond/blastp/meta.yml +++ b/modules/nf-core/diamond/blastp/meta.yml @@ -33,19 +33,24 @@ input: type: file description: File of the indexed DIAMOND database pattern: "*.dmnd" - - - out_ext: - type: string + - - outfmt: + type: integer description: | - Specify the type of output file to be generated. `blast` corresponds to - BLAST pairwise format. `xml` corresponds to BLAST xml format. - `txt` corresponds to to BLAST tabular format. `tsv` corresponds to - taxonomic classification format. - pattern: "blast|xml|txt|daa|sam|tsv|paf" + Specify the type of output file to be generated. + 0, .blast, BLAST pairwise format. + 5, .xml, BLAST XML format. + 6, .txt, BLAST tabular format (default). This format can be customized, the 6 may be followed by a space-separated list of the blast_columns keywords, each specifying a field of the output. + 100, .daa, DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view command. It is also supported by MEGAN and allows a quick import of results. + 101, .sam, SAM format. + 102, .tsv, Taxonomic classification. This format will not print alignments but only a taxonomic classification for each query using the LCA algorithm. + 103, .paf, PAF format. The custom fields in the format are AS (bit score), ZR (raw score) and ZE (e-value). + pattern: "0|5|6|100|101|102|103" - - blast_columns: type: string description: | Optional space separated list of DIAMOND tabular BLAST output keywords - used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: + used in conjunction with the --outfmt 6 option (txt). + Options: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore output: - blast: @@ -54,70 +59,77 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.blast": - type: file + pattern: "*.{blast,blast.gz}" + - "*.{blast,blast.gz}": + type: map description: File containing blastp hits - pattern: "*.{blast}" + pattern: "*.{blast,blast.gz}" - xml: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.xml": - type: file + pattern: "*.{xml,xml.gz}" + - "*.{xml,xml.gz}": + type: map description: File containing blastp hits - pattern: "*.{xml}" + pattern: "*.{xml,xml.gz}" - txt: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.txt": - type: file + pattern: "*.{txt,txt.gz}" + - "*.{txt,txt.gz}": + type: map description: File containing hits in tabular BLAST format. - pattern: "*.{txt}" + pattern: "*.{txt,txt.gz}" - daa: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.daa": - type: file + pattern: "*.{daa,daa.gz}" + - "*.{daa,daa.gz}": + type: map description: File containing hits DAA format - pattern: "*.{daa}" + pattern: "*.{daa,daa.gz}" - sam: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.sam": - type: file + pattern: "*.{sam,sam.gz}" + - "*.{sam,sam.gz}": + type: map description: File containing aligned reads in SAM format - pattern: "*.{sam}" + pattern: "*.{sam,sam.gz}" - tsv: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tsv": - type: file + pattern: "*.{tsv,tsv.gz}" + - "*.{tsv,tsv.gz}": + type: map description: Tab separated file containing taxonomic classification of hits - pattern: "*.{tsv}" + pattern: "*.{tsv,tsv.gz}" - paf: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.paf": - type: file + pattern: "*.{paf,paf.gz}" + - "*.{paf,paf.gz}": + type: map description: File containing aligned reads in pairwise mapping format format - pattern: "*.{paf}" + pattern: "*.{paf,paf.gz}" - versions: - versions.yml: type: file diff --git a/modules/nf-core/diamond/blastp/tests/main.nf.test b/modules/nf-core/diamond/blastp/tests/main.nf.test index f21e926de9d..9211915173c 100644 --- a/modules/nf-core/diamond/blastp/tests/main.nf.test +++ b/modules/nf-core/diamond/blastp/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { } } - test("Should search for protein hits against a DIAMOND db and return a tab separated output file of hits") { + test("sarscov2 - proteome - txt") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] input[1] = DIAMOND_MAKEDB.out.db - input[2] = 'txt' + input[2] = 6 input[3] = 'qseqid qlen' """ } @@ -42,27 +39,20 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.txt, - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } ) } } - test("Should search for zipped protein hits against a DIAMOND db and return a tab separated output file of hits") { + test("sarscov2 - proteome - gz - txt") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) ] input[1] = DIAMOND_MAKEDB.out.db - input[2] = 'txt' + input[2] = 6 input[3] = 'qseqid qlen' """ } @@ -71,27 +61,20 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.txt, - process.out.versions - ).match("gz_txt") - } + { assert snapshot(process.out).match("gz_txt")} ) } } - test("Should search for protein hits against a DIAMOND db and return a daa format file of hits") { + test("sarscov2 - proteome - daa") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] input[1] = DIAMOND_MAKEDB.out.db - input[2] = 'daa' + input[2] = 100 input[3] = [] """ } @@ -101,7 +84,55 @@ nextflow_process { assertAll( { assert process.success }, { assert process.out.daa }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(process.out.versions).match("daa") } + ) + } + + } + + test("sarscov2 - proteome - txt - gz") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] + input[1] = DIAMOND_MAKEDB.out.db + input[2] = 6 + input[3] = 'qseqid qlen' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("txt_gz") } + ) + } + + } + + test("sarscov2 - proteome - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] + input[1] = DIAMOND_MAKEDB.out.db + input[2] = 6 + input[3] = 'qseqid qlen' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } ) } diff --git a/modules/nf-core/diamond/blastp/tests/main.nf.test.snap b/modules/nf-core/diamond/blastp/tests/main.nf.test.snap index e323c8b89c1..44d504337b1 100644 --- a/modules/nf-core/diamond/blastp/tests/main.nf.test.snap +++ b/modules/nf-core/diamond/blastp/tests/main.nf.test.snap @@ -1,54 +1,290 @@ { - "Should search for protein hits against a DIAMOND db and return a tab separated output file of hits": { + "sarscov2 - proteome - txt": { "content": [ - [ - [ - { - "id": "test" - }, - "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "blast": [ + + ], + "daa": [ + + ], + "paf": [ + + ], + "sam": [ + + ], + "tsv": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "versions": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "xml": [ + ] - ], - [ - "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0" - ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2025-01-28T10:25:13.48912978" + }, + "txt_gz": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "blast": [ + + ], + "daa": [ + + ], + "paf": [ + + ], + "sam": [ + + ], + "tsv": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "versions": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "xml": [ + + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-29T14:40:23.906848" + "timestamp": "2025-01-28T10:36:04.361504205" }, "gz_txt": { "content": [ - [ - [ - { - "id": "test" - }, - "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "blast": [ + + ], + "daa": [ + + ], + "paf": [ + + ], + "sam": [ + + ], + "tsv": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt:md5,8131b1afd717f3d5f2f2417c5b562e6e" + ] + ], + "versions": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "xml": [ + ] - ], - [ - "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0" - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-29T14:40:29.865487" + "timestamp": "2025-01-28T10:25:20.993203497" }, - "Should search for protein hits against a DIAMOND db and return a daa format file of hits": { + "daa": { "content": [ [ - "versions.yml:md5,57a0ebeb0a8a732c941ae0102639a9d0" + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2025-01-28T10:25:28.126992812" + }, + "stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "blast": [ + + ], + "daa": [ + + ], + "paf": [ + + ], + "sam": [ + + ], + "tsv": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5f638327037bee3c00e17521c04a652f" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-07-29T14:40:35.362027" + "timestamp": "2025-01-28T10:25:34.911633513" } } \ No newline at end of file diff --git a/modules/nf-core/diamond/blastp/tests/nextflow.config b/modules/nf-core/diamond/blastp/tests/nextflow.config new file mode 100644 index 00000000000..bd28cb1d433 --- /dev/null +++ b/modules/nf-core/diamond/blastp/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: DIAMOND_BLASTP { + ext.args = '--compress 1' + } + +} diff --git a/modules/nf-core/diamond/blastx/environment.yml b/modules/nf-core/diamond/blastx/environment.yml index 950c3c5c55e..60c71ba204e 100644 --- a/modules/nf-core/diamond/blastx/environment.yml +++ b/modules/nf-core/diamond/blastx/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/diamond/cluster/environment.yml b/modules/nf-core/diamond/cluster/environment.yml index 216da62694c..0b70f72fd2b 100644 --- a/modules/nf-core/diamond/cluster/environment.yml +++ b/modules/nf-core/diamond/cluster/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::diamond=2.1.9" + - bioconda::diamond=2.1.9 diff --git a/modules/nf-core/diamond/makedb/environment.yml b/modules/nf-core/diamond/makedb/environment.yml index 950c3c5c55e..60c71ba204e 100644 --- a/modules/nf-core/diamond/makedb/environment.yml +++ b/modules/nf-core/diamond/makedb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/doubletdetection/environment.yml b/modules/nf-core/doubletdetection/environment.yml index 0c4000ce107..a4e8835652d 100644 --- a/modules/nf-core/doubletdetection/environment.yml +++ b/modules/nf-core/doubletdetection/environment.yml @@ -1,13 +1,15 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- conda-forge::anndata=0.10.7 -- conda-forge::louvain=0.8.2 -- conda-forge::numpy=1.26.4 -- conda-forge::pip=24.0 -- conda-forge::python=3.12.3 -- conda-forge::scipy=1.13.1 -- pip -- pip: - - doubletdetection==4.2 + - conda-forge::anndata=0.10.7 + - conda-forge::louvain=0.8.2 + - conda-forge::numpy=1.26.4 + - conda-forge::pip=24.0 + - conda-forge::python=3.12.3 + - conda-forge::scipy=1.13.1 + - pip + - pip: + - doubletdetection==4.2 diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml index 547e6f24a5f..bfd8bfb72a8 100644 --- a/modules/nf-core/dragmap/align/environment.yml +++ b/modules/nf-core/dragmap/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml index 06e608fde72..abd4d3f261e 100644 --- a/modules/nf-core/dragmap/hashtable/environment.yml +++ b/modules/nf-core/dragmap/hashtable/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dragonflye/environment.yml b/modules/nf-core/dragonflye/environment.yml index 6111fba13b7..7b7ed83ad0b 100644 --- a/modules/nf-core/dragonflye/environment.yml +++ b/modules/nf-core/dragonflye/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dshbio/exportsegments/environment.yml b/modules/nf-core/dshbio/exportsegments/environment.yml index cd022f8776b..a047db00d83 100644 --- a/modules/nf-core/dshbio/exportsegments/environment.yml +++ b/modules/nf-core/dshbio/exportsegments/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dshbio/filterbed/environment.yml b/modules/nf-core/dshbio/filterbed/environment.yml index cd022f8776b..a047db00d83 100644 --- a/modules/nf-core/dshbio/filterbed/environment.yml +++ b/modules/nf-core/dshbio/filterbed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dshbio/filtergff3/environment.yml b/modules/nf-core/dshbio/filtergff3/environment.yml index cd022f8776b..a047db00d83 100644 --- a/modules/nf-core/dshbio/filtergff3/environment.yml +++ b/modules/nf-core/dshbio/filtergff3/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dshbio/splitbed/environment.yml b/modules/nf-core/dshbio/splitbed/environment.yml index cd022f8776b..a047db00d83 100644 --- a/modules/nf-core/dshbio/splitbed/environment.yml +++ b/modules/nf-core/dshbio/splitbed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dshbio/splitgff3/environment.yml b/modules/nf-core/dshbio/splitgff3/environment.yml index cd022f8776b..a047db00d83 100644 --- a/modules/nf-core/dshbio/splitgff3/environment.yml +++ b/modules/nf-core/dshbio/splitgff3/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/duphold/environment.yml b/modules/nf-core/duphold/environment.yml index d607f1f48ef..3afda823b1e 100644 --- a/modules/nf-core/duphold/environment.yml +++ b/modules/nf-core/duphold/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index fb16938d202..0add73e8168 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-dupradar=1.32.0" + - bioconda::bioconductor-dupradar=1.32.0 diff --git a/modules/nf-core/dysgu/environment.yml b/modules/nf-core/dysgu/environment.yml index cbf7a7668df..8f42ba37a5a 100644 --- a/modules/nf-core/dysgu/environment.yml +++ b/modules/nf-core/dysgu/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ectyper/environment.yml b/modules/nf-core/ectyper/environment.yml index 7e7f57a874d..a0b3d6f3902 100644 --- a/modules/nf-core/ectyper/environment.yml +++ b/modules/nf-core/ectyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/eggnogmapper/environment.yml b/modules/nf-core/eggnogmapper/environment.yml index 2092ea512ba..6e6e0699876 100644 --- a/modules/nf-core/eggnogmapper/environment.yml +++ b/modules/nf-core/eggnogmapper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/eido/convert/environment.yml b/modules/nf-core/eido/convert/environment.yml index 11ca69f4353..b4fd9081b72 100644 --- a/modules/nf-core/eido/convert/environment.yml +++ b/modules/nf-core/eido/convert/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/eido/validate/environment.yml b/modules/nf-core/eido/validate/environment.yml index 1bbd80bb62f..255240229b8 100644 --- a/modules/nf-core/eido/validate/environment.yml +++ b/modules/nf-core/eido/validate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml index 40586837948..4708a34725f 100644 --- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml +++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/eklipse/environment.yml b/modules/nf-core/eklipse/environment.yml index b638fba1d1d..5598fc8afc0 100644 --- a/modules/nf-core/eklipse/environment.yml +++ b/modules/nf-core/eklipse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/elprep/fastatoelfasta/environment.yml b/modules/nf-core/elprep/fastatoelfasta/environment.yml index 6ab3f8fc5d7..3df24fb0cc3 100644 --- a/modules/nf-core/elprep/fastatoelfasta/environment.yml +++ b/modules/nf-core/elprep/fastatoelfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::elprep=5.1.3" + - bioconda::elprep=5.1.3 diff --git a/modules/nf-core/elprep/filter/environment.yml b/modules/nf-core/elprep/filter/environment.yml index 38dd4f4724b..3df24fb0cc3 100644 --- a/modules/nf-core/elprep/filter/environment.yml +++ b/modules/nf-core/elprep/filter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/elprep/merge/environment.yml b/modules/nf-core/elprep/merge/environment.yml index 841e7cdb7bb..29842cbf397 100644 --- a/modules/nf-core/elprep/merge/environment.yml +++ b/modules/nf-core/elprep/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/elprep/split/environment.yml b/modules/nf-core/elprep/split/environment.yml index 38dd4f4724b..3df24fb0cc3 100644 --- a/modules/nf-core/elprep/split/environment.yml +++ b/modules/nf-core/elprep/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/emboss/cons/environment.yml b/modules/nf-core/emboss/cons/environment.yml index 6c075a72d92..39facd5b4c9 100644 --- a/modules/nf-core/emboss/cons/environment.yml +++ b/modules/nf-core/emboss/cons/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/emboss/revseq/environment.yml b/modules/nf-core/emboss/revseq/environment.yml index 6c075a72d92..39facd5b4c9 100644 --- a/modules/nf-core/emboss/revseq/environment.yml +++ b/modules/nf-core/emboss/revseq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/emboss/seqret/environment.yml b/modules/nf-core/emboss/seqret/environment.yml index 6c075a72d92..39facd5b4c9 100644 --- a/modules/nf-core/emboss/seqret/environment.yml +++ b/modules/nf-core/emboss/seqret/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/emmtyper/environment.yml b/modules/nf-core/emmtyper/environment.yml index 93aed9cf50f..7aa11d0cbaa 100644 --- a/modules/nf-core/emmtyper/environment.yml +++ b/modules/nf-core/emmtyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/endorspy/environment.yml b/modules/nf-core/endorspy/environment.yml index fea7004305f..a94a925d9a7 100644 --- a/modules/nf-core/endorspy/environment.yml +++ b/modules/nf-core/endorspy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index 3d36eb17c0c..cac59e88206 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/environment.yml b/modules/nf-core/ensemblvep/environment.yml index e94bfeb2cb0..c44c0a753d5 100644 --- a/modules/nf-core/ensemblvep/environment.yml +++ b/modules/nf-core/ensemblvep/environment.yml @@ -1,5 +1,5 @@ -# You can use this file to create a conda environment for this module: -# conda env create -f environment.yml +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 3d36eb17c0c..cac59e88206 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 3d36eb17c0c..cac59e88206 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/entrezdirect/esearch/environment.yml b/modules/nf-core/entrezdirect/esearch/environment.yml index 4aee27d35c8..b6d83e9a4f7 100644 --- a/modules/nf-core/entrezdirect/esearch/environment.yml +++ b/modules/nf-core/entrezdirect/esearch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/entrezdirect/esummary/environment.yml b/modules/nf-core/entrezdirect/esummary/environment.yml index 4aee27d35c8..b6d83e9a4f7 100644 --- a/modules/nf-core/entrezdirect/esummary/environment.yml +++ b/modules/nf-core/entrezdirect/esummary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/entrezdirect/xtract/environment.yml b/modules/nf-core/entrezdirect/xtract/environment.yml index 4aee27d35c8..b6d83e9a4f7 100644 --- a/modules/nf-core/entrezdirect/xtract/environment.yml +++ b/modules/nf-core/entrezdirect/xtract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/epang/place/environment.yml b/modules/nf-core/epang/place/environment.yml index 6faa55f390e..28ae4fc9613 100644 --- a/modules/nf-core/epang/place/environment.yml +++ b/modules/nf-core/epang/place/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/epang/split/environment.yml b/modules/nf-core/epang/split/environment.yml index 6faa55f390e..28ae4fc9613 100644 --- a/modules/nf-core/epang/split/environment.yml +++ b/modules/nf-core/epang/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/evigene/tr2aacds/environment.yml b/modules/nf-core/evigene/tr2aacds/environment.yml index ee044641397..88b9f8a9617 100644 --- a/modules/nf-core/evigene/tr2aacds/environment.yml +++ b/modules/nf-core/evigene/tr2aacds/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::evigene=23.7.15" + - bioconda::evigene=23.7.15 diff --git a/modules/nf-core/expansionhunter/environment.yml b/modules/nf-core/expansionhunter/environment.yml index 07db4374d40..951de76c060 100644 --- a/modules/nf-core/expansionhunter/environment.yml +++ b/modules/nf-core/expansionhunter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/expansionhunterdenovo/merge/environment.yml b/modules/nf-core/expansionhunterdenovo/merge/environment.yml index da1383d5349..c39c8171502 100644 --- a/modules/nf-core/expansionhunterdenovo/merge/environment.yml +++ b/modules/nf-core/expansionhunterdenovo/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/expansionhunterdenovo/profile/environment.yml b/modules/nf-core/expansionhunterdenovo/profile/environment.yml index da1383d5349..c39c8171502 100644 --- a/modules/nf-core/expansionhunterdenovo/profile/environment.yml +++ b/modules/nf-core/expansionhunterdenovo/profile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/falco/environment.yml b/modules/nf-core/falco/environment.yml index c48809ccc67..59c973a986a 100644 --- a/modules/nf-core/falco/environment.yml +++ b/modules/nf-core/falco/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/famsa/align/environment.yml b/modules/nf-core/famsa/align/environment.yml index 08b6f88908a..7553f17dbfb 100644 --- a/modules/nf-core/famsa/align/environment.yml +++ b/modules/nf-core/famsa/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/famsa/guidetree/environment.yml b/modules/nf-core/famsa/guidetree/environment.yml index 08b6f88908a..7553f17dbfb 100644 --- a/modules/nf-core/famsa/guidetree/environment.yml +++ b/modules/nf-core/famsa/guidetree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/faqcs/environment.yml b/modules/nf-core/faqcs/environment.yml index d019c4f8bfb..23f39ad6dca 100644 --- a/modules/nf-core/faqcs/environment.yml +++ b/modules/nf-core/faqcs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fargene/environment.yml b/modules/nf-core/fargene/environment.yml index ade4d77097e..197b2b32ba7 100644 --- a/modules/nf-core/fargene/environment.yml +++ b/modules/nf-core/fargene/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fast2q/environment.yml b/modules/nf-core/fast2q/environment.yml new file mode 100644 index 00000000000..8da3a91928a --- /dev/null +++ b/modules/nf-core/fast2q/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::fast2q=2.7.2 diff --git a/modules/nf-core/fast2q/main.nf b/modules/nf-core/fast2q/main.nf new file mode 100644 index 00000000000..6ecd725162f --- /dev/null +++ b/modules/nf-core/fast2q/main.nf @@ -0,0 +1,67 @@ +process FAST2Q { + + tag "2FAST2Q" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fast2q:2.7.2--pyh7e72e81_0' : + 'biocontainers/fast2q:2.7.2--pyh7e72e81_0' }" + + input: + tuple val(meta), path(fastq) + tuple val(meta2), path(library) + + output: + tuple val(meta), path("${prefix}.csv") , emit: count_matrix + tuple val(meta), path("${prefix}_stats.csv") , emit: stats + tuple val(meta), path("${prefix}_distribution_plot.png") , emit: distribution_plot + tuple val(meta), path("${prefix}_reads_plot.png") , emit: reads_plot + tuple val(meta), path("${prefix}_reads_plot_percentage.png"), emit: reads_plot_percentage + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def input_file = (fastq instanceof Path && fastq.exists()) ? "--s ${fastq}" : '' + def library_file = (library instanceof Path && library.exists()) ? "--g ${library}" : '' + + """ + export MPLCONFIGDIR=\$PWD + 2fast2q \\ + -c \\ + --o ./ \\ + --fn ${prefix} \\ + --cp ${task.cpus} \\ + $input_file \\ + $library_file \\ + $args + + mv **/${prefix}* . + + cat <<-END_VERSIONS > versions.yml + ${task.process}: + 2FAST2Q version: \$(2fast2q -v | grep 'Version:' | sed 's/Version: //g') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.csv + touch ${prefix}_stats.csv + touch ${prefix}_distribution_plot.png + touch ${prefix}_reads_plot.png + touch ${prefix}_reads_plot_percentage.png + + cat <<-END_VERSIONS > versions.yml + ${task.process}: + 2FAST2Q version: \$(2fast2q -v | grep 'Version:' | sed 's/Version: //g') + END_VERSIONS + """ + +} diff --git a/modules/nf-core/fast2q/meta.yml b/modules/nf-core/fast2q/meta.yml new file mode 100644 index 00000000000..93619bde89a --- /dev/null +++ b/modules/nf-core/fast2q/meta.yml @@ -0,0 +1,98 @@ +name: fast2q +description: A program that counts sequence occurrences in FASTQ files. +keywords: + - CRISPRi + - FASTQ + - genomics +tools: + - 2FAST2Q: + description: | + 2FAST2Q is ideal for CRISPRi-Seq, and for extracting and counting any kind of information from reads in the fastq format, such as barcodes in Bar-seq experiments. + 2FAST2Q can work with sequence mismatches, Phred-score, and be used to find and extract unknown sequences delimited by known sequences. + 2FAST2Q can extract multiple features per read using either fixed positions or delimiting search sequences. + homepage: https://github.com/afombravo/2FAST2Q + doi: 10.7717/peerj.14041 + licence: ["GPL-3.0-or-later"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test'] + - fastq: + type: directory + description: Folder with FASTQ file(s). 2FAST2Q automatically picks up all the FASTQ files inside the provided folder. + pattern: "*.{fastq,gz}" + + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'library_name', multiple_features_per_read:false ] + - library: + type: file + description: .csv library file following the ´Feature_name,sequence´ or ´Feature_name,sequence1:sequence2´ format. See 2FAST2Q instructions for more information. + pattern: "*.csv" + +output: + - count_matrix: + - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test' ] + - ${prefix}.csv: + type: file + description: | + Count matrix csv file + - stats: + - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test' ] + - ${prefix}_stats.csv: + type: file + description: | + File containing all the relevant statistics such as quality passing reads, aligned reads, total reads, and sample run times. + - distribution_plot: + - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test' ] + - ${prefix}_distribution_plot.png: + type: file + description: | + Violin plot of the distribution of reads per feature across all samples. + - reads_plot: + - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test' ] + - ${prefix}_reads_plot.png: + type: file + description: | + Bar plot with the distribution of reads, in absolute numbers, binned to the different quality metrics indicated in the statistics.csv + - reads_plot_percentage: + - meta: + type: map + description: | + Groovy Map containing output name. + e.g. [ id:'test' ] + - ${prefix}_reads_plot_percentage.png: + type: file + description: | + Bar plot with the distribution of reads, in percentage, binned to the different quality metrics indicated in the statistics.csv + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@afombravo" +maintainers: + - "@afombravo" diff --git a/modules/nf-core/fast2q/tests/main.nf.test b/modules/nf-core/fast2q/tests/main.nf.test new file mode 100644 index 00000000000..b0f985f1779 --- /dev/null +++ b/modules/nf-core/fast2q/tests/main.nf.test @@ -0,0 +1,165 @@ +nextflow_process { + + name "Test Process 2FAST2Q" + script "../main.nf" + process "FAST2Q" + + tag "modules" + tag "modules_nfcore" + tag "fast2q" + + config './nextflow.config' + + test("2FAST2Q self-test") { + + when { + + params { + module_args = '-t' + } + + process { + """ + input[0] = [ + [ id:'test1' ], // meta map + [] + ] + input[1] = [ + [ id:'library_name', multiple_features_per_read:false ], // meta map for second input + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.count_matrix, + file(process.out.stats[0][1]).name, + file(process.out.distribution_plot[0][1]).name, + file(process.out.reads_plot[0][1]).name, + file(process.out.reads_plot_percentage[0][1]).name, + process.out.versions, // versions file + path(process.out.versions[0]).yaml // Validate against the versions snapshot + ).match() + } + ) + } + } + + test("Extracting and counting all features at position=0 with default length of 20bp from a FASTQ file (without optional library.csv)") { + + when { + + params { + module_args = '--mo EC' + } + + process { + """ + input[0] = [ + [ id:'test1' ], // meta map + file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file + ] + input[1] = [ + [ id:'library_name', multiple_features_per_read:false ], // meta map for second input + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, // Ensure process ran successfully + { assert snapshot( + process.out.count_matrix, + file(process.out.stats[0][1]).name, + file(process.out.distribution_plot[0][1]).name, + file(process.out.reads_plot[0][1]).name, + file(process.out.reads_plot_percentage[0][1]).name, + process.out.versions, // versions file + path(process.out.versions[0]).yaml // Validate against the versions snapshot + ).match() + } + ) + } + } + + test("Extracting all features at position=0 with default length of 20bp from a FASTQ file, and respective alignment to a file with DNA features (library.csv)") { + + when { + + params { + module_args = '' + } + + process { + """ + input[0] = [ + [ id:'test1' ], // meta map + file(params.test_data_base + '/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz', checkIfExists: true) // FASTQ file + ] + input[1] = [ + [ id:'library_name', multiple_features_per_read:false ], // meta map for second input + file(params.test_data_base + '/data/genomics/mus_musculus/mageck/yusa_library.csv', checkIfExists: true) // library file + ] + """ + } + } + + then { + assertAll( + { assert process.success }, // Ensure process ran successfully + { assert snapshot( + process.out.count_matrix, + file(process.out.stats[0][1]).name, + file(process.out.distribution_plot[0][1]).name, + file(process.out.reads_plot[0][1]).name, + file(process.out.reads_plot_percentage[0][1]).name, + process.out.versions, // versions file + path(process.out.versions[0]).yaml // Validate against the versions snapshot + ).match() + } + ) + } + } + + test("2FAST2Q self-test - stub") { + options "-stub" + when { + + params { + module_args = '-t' + } + + process { + """ + input[0] = [ + [ id:'test1' ], // meta map + [] + ] + input[1] = [ + [ id:'library_name', multiple_features_per_read:false ], // meta map for second input + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml // Validate against the versions snapshot + ).match() + } + ) + } + } + + +} diff --git a/modules/nf-core/fast2q/tests/main.nf.test.snap b/modules/nf-core/fast2q/tests/main.nf.test.snap new file mode 100644 index 00000000000..2e3220584de --- /dev/null +++ b/modules/nf-core/fast2q/tests/main.nf.test.snap @@ -0,0 +1,191 @@ +{ + "2FAST2Q self-test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test1" + }, + "test1.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test1" + }, + "test1_stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test1" + }, + "test1_distribution_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test1" + }, + "test1_reads_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test1" + }, + "test1_reads_plot_percentage.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,996f5cbd9c8055ac57bd83b5278c20a7" + ], + "count_matrix": [ + [ + { + "id": "test1" + }, + "test1.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "distribution_plot": [ + [ + { + "id": "test1" + }, + "test1_distribution_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads_plot": [ + [ + { + "id": "test1" + }, + "test1_reads_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads_plot_percentage": [ + [ + { + "id": "test1" + }, + "test1_reads_plot_percentage.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test1" + }, + "test1_stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,996f5cbd9c8055ac57bd83b5278c20a7" + ] + }, + { + "FAST2Q": { + "2FAST2Q version": "2.7.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-28T20:56:17.951393012" + }, + "Extracting and counting all features at position=0 with default length of 20bp from a FASTQ file (without optional library.csv)": { + "content": [ + [ + [ + { + "id": "test1" + }, + "test1.csv:md5,a1ead6bcda7e3de46ae53846aca71a41" + ] + ], + "test1_stats.csv", + "test1_distribution_plot.png", + "test1_reads_plot.png", + "test1_reads_plot_percentage.png", + [ + "versions.yml:md5,996f5cbd9c8055ac57bd83b5278c20a7" + ], + { + "FAST2Q": { + "2FAST2Q version": "2.7.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-28T21:03:48.898136957" + }, + "Extracting all features at position=0 with default length of 20bp from a FASTQ file, and respective alignment to a file with DNA features (library.csv)": { + "content": [ + [ + [ + { + "id": "test1" + }, + "test1.csv:md5,caae8adb0277f74259f2b39c407909a8" + ] + ], + "test1_stats.csv", + "test1_distribution_plot.png", + "test1_reads_plot.png", + "test1_reads_plot_percentage.png", + [ + "versions.yml:md5,996f5cbd9c8055ac57bd83b5278c20a7" + ], + { + "FAST2Q": { + "2FAST2Q version": "2.7.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-28T21:04:15.318640256" + }, + "2FAST2Q self-test": { + "content": [ + [ + [ + { + "id": "test1" + }, + "test1.csv:md5,22686579ca39d81107b7889cc87c3865" + ] + ], + "test1_stats.csv", + "test1_distribution_plot.png", + "test1_reads_plot.png", + "test1_reads_plot_percentage.png", + [ + "versions.yml:md5,996f5cbd9c8055ac57bd83b5278c20a7" + ], + { + "FAST2Q": { + "2FAST2Q version": "2.7.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-28T21:03:27.680008475" + } +} diff --git a/modules/nf-core/fast2q/tests/nextflow.config b/modules/nf-core/fast2q/tests/nextflow.config new file mode 100644 index 00000000000..ecb6df3b52c --- /dev/null +++ b/modules/nf-core/fast2q/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'FAST2Q' { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/fast2q/tests/tags.yml b/modules/nf-core/fast2q/tests/tags.yml new file mode 100644 index 00000000000..c41363f4039 --- /dev/null +++ b/modules/nf-core/fast2q/tests/tags.yml @@ -0,0 +1,2 @@ +fast2q: + - "modules/nf-core/fast2q/**" diff --git a/modules/nf-core/fastani/environment.yml b/modules/nf-core/fastani/environment.yml index bcfc7b4a1be..25c0180f049 100644 --- a/modules/nf-core/fastani/environment.yml +++ b/modules/nf-core/fastani/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastavalidator/environment.yml b/modules/nf-core/fastavalidator/environment.yml index 44d55c1faf9..effc5be46a9 100644 --- a/modules/nf-core/fastavalidator/environment.yml +++ b/modules/nf-core/fastavalidator/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::py_fasta_validator=0.6" + - bioconda::py_fasta_validator=0.6 diff --git a/modules/nf-core/fastawindows/environment.yml b/modules/nf-core/fastawindows/environment.yml index 6775fb2e6ff..787f1e648fc 100644 --- a/modules/nf-core/fastawindows/environment.yml +++ b/modules/nf-core/fastawindows/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastk/fastk/environment.yml b/modules/nf-core/fastk/fastk/environment.yml index 14207ff69ae..d8cc5f8e4f7 100644 --- a/modules/nf-core/fastk/fastk/environment.yml +++ b/modules/nf-core/fastk/fastk/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::false_flag # False flag to pass nf-core/lint + - bioconda::false_flag diff --git a/modules/nf-core/fastk/histex/environment.yml b/modules/nf-core/fastk/histex/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/fastk/histex/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/fastk/merge/environment.yml b/modules/nf-core/fastk/merge/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/fastk/merge/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/fastme/environment.yml b/modules/nf-core/fastme/environment.yml index 4a69cb341f9..1e258b4b9f3 100644 --- a/modules/nf-core/fastme/environment.yml +++ b/modules/nf-core/fastme/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastme=2.1.6.1" + - bioconda::fastme=2.1.6.1 diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 26d4aca5ddd..c9bc4d02451 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c7638f..f9f54ee9b43 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqe/environment.yml b/modules/nf-core/fastqe/environment.yml index 0b98f6fc33b..1ec2395c10b 100644 --- a/modules/nf-core/fastqe/environment.yml +++ b/modules/nf-core/fastqe/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastqe=0.3.3" + - bioconda::fastqe=0.3.3 diff --git a/modules/nf-core/fastqscan/environment.yml b/modules/nf-core/fastqscan/environment.yml index a041ef99ec8..b372c857d2a 100644 --- a/modules/nf-core/fastqscan/environment.yml +++ b/modules/nf-core/fastqscan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml index 85764e0d22b..3b3ba5213e6 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastq-screen=0.15.3" + - bioconda::fastq-screen=0.15.3 diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml index c63c61e206a..14c2a273d5a 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastq-screen=0.15.3" + - bioconda::fastq-screen=0.15.3 - bioconda::perl-gdgraph=1.54 diff --git a/modules/nf-core/fasttree/environment.yml b/modules/nf-core/fasttree/environment.yml index abe21b5a032..48f9ff8ec8e 100644 --- a/modules/nf-core/fasttree/environment.yml +++ b/modules/nf-core/fasttree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastx/collapser/environment.yml b/modules/nf-core/fastx/collapser/environment.yml index bc0c3eb35a2..9df13c61022 100644 --- a/modules/nf-core/fastx/collapser/environment.yml +++ b/modules/nf-core/fastx/collapser/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastx_toolkit=0.0.14" + - bioconda::fastx_toolkit=0.0.14 diff --git a/modules/nf-core/fcs/fcsadaptor/environment.yml b/modules/nf-core/fcs/fcsadaptor/environment.yml index 14207ff69ae..d8cc5f8e4f7 100644 --- a/modules/nf-core/fcs/fcsadaptor/environment.yml +++ b/modules/nf-core/fcs/fcsadaptor/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::false_flag # False flag to pass nf-core/lint + - bioconda::false_flag diff --git a/modules/nf-core/fcs/fcsgx/environment.yml b/modules/nf-core/fcs/fcsgx/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/fcs/fcsgx/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/fcsgx/cleangenome/environment.yml b/modules/nf-core/fcsgx/cleangenome/environment.yml index 8fbbad1b543..918383951db 100644 --- a/modules/nf-core/fcsgx/cleangenome/environment.yml +++ b/modules/nf-core/fcsgx/cleangenome/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ncbi-fcs-gx=0.5.4" + - bioconda::ncbi-fcs-gx=0.5.4 diff --git a/modules/nf-core/fcsgx/fetchdb/environment.yml b/modules/nf-core/fcsgx/fetchdb/environment.yml index 8fbbad1b543..918383951db 100644 --- a/modules/nf-core/fcsgx/fetchdb/environment.yml +++ b/modules/nf-core/fcsgx/fetchdb/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ncbi-fcs-gx=0.5.4" + - bioconda::ncbi-fcs-gx=0.5.4 diff --git a/modules/nf-core/fcsgx/rungx/environment.yml b/modules/nf-core/fcsgx/rungx/environment.yml index 8fbbad1b543..918383951db 100644 --- a/modules/nf-core/fcsgx/rungx/environment.yml +++ b/modules/nf-core/fcsgx/rungx/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ncbi-fcs-gx=0.5.4" + - bioconda::ncbi-fcs-gx=0.5.4 diff --git a/modules/nf-core/ffq/environment.yml b/modules/nf-core/ffq/environment.yml index 14c2f80f07a..a0c2b7f9222 100644 --- a/modules/nf-core/ffq/environment.yml +++ b/modules/nf-core/ffq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml index aa73390d8fa..553d54d428e 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fgbio=2.4.0" - - "conda-forge::r-ggplot2=3.5.1" + - bioconda::fgbio=2.4.0 + - conda-forge::r-ggplot2=3.5.1 diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/fastqtobam/environment.yml +++ b/modules/nf-core/fgbio/fastqtobam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/filterconsensusreads/environment.yml b/modules/nf-core/fgbio/filterconsensusreads/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/filterconsensusreads/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/sortbam/environment.yml b/modules/nf-core/fgbio/sortbam/environment.yml index 562a945934b..340843778c4 100644 --- a/modules/nf-core/fgbio/sortbam/environment.yml +++ b/modules/nf-core/fgbio/sortbam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fgbio/zipperbams/environment.yml b/modules/nf-core/fgbio/zipperbams/environment.yml index e2c4b144f32..4ebc0924d7b 100644 --- a/modules/nf-core/fgbio/zipperbams/environment.yml +++ b/modules/nf-core/fgbio/zipperbams/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/filtlong/environment.yml b/modules/nf-core/filtlong/environment.yml index 746c83a45cc..1efde8ebc7d 100644 --- a/modules/nf-core/filtlong/environment.yml +++ b/modules/nf-core/filtlong/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/find/concatenate/meta.yml b/modules/nf-core/find/concatenate/meta.yml index bef1c2a5b5b..4978e05beb0 100644 --- a/modules/nf-core/find/concatenate/meta.yml +++ b/modules/nf-core/find/concatenate/meta.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "find_concatenate" -description: A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size +description: A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size keywords: - concatenate - gzip @@ -19,7 +19,7 @@ tools: documentation: https://man7.org/linux/man-pages/man1/find.1.html licence: ["other"] identifier: "" - + input: - - meta: type: map diff --git a/modules/nf-core/find/unpigz/environment.yml b/modules/nf-core/find/unpigz/environment.yml index 596e4cc5bb2..0dfaec7760e 100644 --- a/modules/nf-core/find/unpigz/environment.yml +++ b/modules/nf-core/find/unpigz/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/find/unpigz/main.nf b/modules/nf-core/find/unpigz/main.nf index 6bff718ac03..a51186461ef 100644 --- a/modules/nf-core/find/unpigz/main.nf +++ b/modules/nf-core/find/unpigz/main.nf @@ -11,7 +11,7 @@ process FIND_UNPIGZ { tuple val(meta), path(files_in, stageAs: 'gzipped/*', arity: '1..*') output: - tuple val(meta), path("${prefix}.*"), emit: file_out + tuple val(meta), path("ungzipped/*"), emit: file_out path "versions.yml", emit: versions when: @@ -19,20 +19,20 @@ process FIND_UNPIGZ { script: def args = task.ext.args ?: "" - prefix = task.ext.prefix ?: "${meta.id}" if (files_in.any { file -> !file.name.endsWith('.gz') }) { error("All files provided to this module must be gzipped (and have the .gz extension).") } """ + mkdir -p ungzipped while IFS= read -r -d \$'\\0' file; do unpigz \\ ${args} \\ -cd \\ --processes ${task.cpus} \\ \$file \\ - > ${prefix}.\$( basename \$file .gz ) + > ungzipped/\$( basename \$file .gz ) done < <( find gzipped/ -name '*.gz' -print0 ) cat <<-END_VERSIONS > versions.yml @@ -43,9 +43,9 @@ process FIND_UNPIGZ { """ stub: - prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.test_file.txt + mkdir -p ungzipped + touch ungzipped/test_file.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/find/unpigz/meta.yml b/modules/nf-core/find/unpigz/meta.yml index 01775e5e75b..6367ba323a3 100644 --- a/modules/nf-core/find/unpigz/meta.yml +++ b/modules/nf-core/find/unpigz/meta.yml @@ -12,12 +12,14 @@ tools: by evaluating the given expression documentation: https://man7.org/linux/man-pages/man1/find.1.html licence: ["GPL-3.0-or-later"] + identifier: "" - pigz: description: pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. documentation: https://zlib.net/pigz/pigz.pdf licence: ["other"] + identifier: "" input: - - meta: @@ -37,17 +39,17 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - ${prefix}.*: + pattern: "*" + - ungzipped/*: type: file - description: Decompressed files - pattern: "${prefix}.*" - + description: | + Files that have been decompressed + pattern: "*" - versions: - - "versions.yml": + - versions.yml: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@Biowilko" maintainers: diff --git a/modules/nf-core/find/unpigz/tests/main.nf.test b/modules/nf-core/find/unpigz/tests/main.nf.test index e23cfc35ea0..f4c550157c3 100644 --- a/modules/nf-core/find/unpigz/tests/main.nf.test +++ b/modules/nf-core/find/unpigz/tests/main.nf.test @@ -31,7 +31,10 @@ nextflow_process { process.out, process.out.versions ).match() - } + }, + { assert process.out.file_out[0][1].size() == 2 }, + { assert file(process.out.file_out[0][1].find { file(it).name == "genome.gff3" }).exists() }, + { assert file(process.out.file_out[0][1].find { file(it).name == "contigs.genome.maf" }).exists() }, ) } } diff --git a/modules/nf-core/find/unpigz/tests/main.nf.test.snap b/modules/nf-core/find/unpigz/tests/main.nf.test.snap index a75ecfcd4a6..c08049f2331 100644 --- a/modules/nf-core/find/unpigz/tests/main.nf.test.snap +++ b/modules/nf-core/find/unpigz/tests/main.nf.test.snap @@ -3,20 +3,20 @@ "content": [ { "0": [ - + ], "1": [ - + ], "file_out": [ - + ], "versions": [ - + ] }, [ - + ] ], "meta": { @@ -35,8 +35,8 @@ "single_end": true }, [ - "test.contigs.genome.maf:md5,caebfb2c47ffb50b1e64d5520dddd5d2", - "test.genome.gff3:md5,357435a81a9981a0128e840ebe11051e" + "contigs.genome.maf:md5,caebfb2c47ffb50b1e64d5520dddd5d2", + "genome.gff3:md5,357435a81a9981a0128e840ebe11051e" ] ] ], @@ -50,8 +50,8 @@ "single_end": true }, [ - "test.contigs.genome.maf:md5,caebfb2c47ffb50b1e64d5520dddd5d2", - "test.genome.gff3:md5,357435a81a9981a0128e840ebe11051e" + "contigs.genome.maf:md5,caebfb2c47ffb50b1e64d5520dddd5d2", + "genome.gff3:md5,357435a81a9981a0128e840ebe11051e" ] ] ], @@ -67,7 +67,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-29T11:41:14.076548" + "timestamp": "2025-02-03T12:43:14.808936" }, "test_stub": { "content": [ @@ -78,7 +78,7 @@ "id": "test", "single_end": true }, - "test.test_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -90,7 +90,7 @@ "id": "test", "single_end": true }, - "test.test_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -105,7 +105,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-29T11:56:40.312202" + "timestamp": "2025-02-03T12:45:47.60277" }, "test_unpigz_success_single_file": { "content": [ @@ -116,7 +116,7 @@ "id": "test", "single_end": true }, - "test.genome.gff3:md5,357435a81a9981a0128e840ebe11051e" + "genome.gff3:md5,357435a81a9981a0128e840ebe11051e" ] ], "1": [ @@ -128,7 +128,7 @@ "id": "test", "single_end": true }, - "test.genome.gff3:md5,357435a81a9981a0128e840ebe11051e" + "genome.gff3:md5,357435a81a9981a0128e840ebe11051e" ] ], "versions": [ @@ -143,6 +143,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-29T11:54:16.396814" + "timestamp": "2025-02-03T12:43:23.437129" } -} \ No newline at end of file +} diff --git a/modules/nf-core/flash/environment.yml b/modules/nf-core/flash/environment.yml index eb575fc52ab..ade7f552489 100644 --- a/modules/nf-core/flash/environment.yml +++ b/modules/nf-core/flash/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/flye/environment.yml b/modules/nf-core/flye/environment.yml index 87b97eb89b8..cbad0b1c13a 100644 --- a/modules/nf-core/flye/environment.yml +++ b/modules/nf-core/flye/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldcomp/compress/environment.yml b/modules/nf-core/foldcomp/compress/environment.yml index b061ede4c8b..1b108167513 100644 --- a/modules/nf-core/foldcomp/compress/environment.yml +++ b/modules/nf-core/foldcomp/compress/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::foldcomp=0.0.7" + - bioconda::foldcomp=0.0.7 diff --git a/modules/nf-core/foldcomp/decompress/environment.yml b/modules/nf-core/foldcomp/decompress/environment.yml index b061ede4c8b..1b108167513 100644 --- a/modules/nf-core/foldcomp/decompress/environment.yml +++ b/modules/nf-core/foldcomp/decompress/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::foldcomp=0.0.7" + - bioconda::foldcomp=0.0.7 diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml index 80d4dd371d9..9d5d3b05d0f 100644 --- a/modules/nf-core/foldmason/createdb/environment.yml +++ b/modules/nf-core/foldmason/createdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml index fa2909a9491..7462add6687 100644 --- a/modules/nf-core/foldmason/easymsa/environment.yml +++ b/modules/nf-core/foldmason/easymsa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldmason/msa2lddtreport/environment.yml b/modules/nf-core/foldmason/msa2lddtreport/environment.yml index 80d4dd371d9..9d5d3b05d0f 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/environment.yml +++ b/modules/nf-core/foldmason/msa2lddtreport/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldseek/createdb/environment.yml b/modules/nf-core/foldseek/createdb/environment.yml index c59ddfe54d7..8aee2e5adec 100644 --- a/modules/nf-core/foldseek/createdb/environment.yml +++ b/modules/nf-core/foldseek/createdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json name: foldseek_createdb channels: - conda-forge diff --git a/modules/nf-core/foldseek/easysearch/environment.yml b/modules/nf-core/foldseek/easysearch/environment.yml index c38d477d0c4..18b651fed56 100644 --- a/modules/nf-core/foldseek/easysearch/environment.yml +++ b/modules/nf-core/foldseek/easysearch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json name: foldseek_easysearch channels: - conda-forge diff --git a/modules/nf-core/fq/generate/environment.yml b/modules/nf-core/fq/generate/environment.yml index 74b146083b5..0a86d11be38 100644 --- a/modules/nf-core/fq/generate/environment.yml +++ b/modules/nf-core/fq/generate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fq/lint/environment.yml b/modules/nf-core/fq/lint/environment.yml index 74b146083b5..0a86d11be38 100644 --- a/modules/nf-core/fq/lint/environment.yml +++ b/modules/nf-core/fq/lint/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index 74b146083b5..0a86d11be38 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fqtk/environment.yml b/modules/nf-core/fqtk/environment.yml index 90897712ab3..6cde1d81bae 100644 --- a/modules/nf-core/fqtk/environment.yml +++ b/modules/nf-core/fqtk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/freebayes/environment.yml b/modules/nf-core/freebayes/environment.yml index 3f593696808..8f1878ef42d 100644 --- a/modules/nf-core/freebayes/environment.yml +++ b/modules/nf-core/freebayes/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/freyja/boot/environment.yml b/modules/nf-core/freyja/boot/environment.yml index 69da13f76f3..0b5b6b06f37 100644 --- a/modules/nf-core/freyja/boot/environment.yml +++ b/modules/nf-core/freyja/boot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/freyja/demix/environment.yml b/modules/nf-core/freyja/demix/environment.yml index 69da13f76f3..0b5b6b06f37 100644 --- a/modules/nf-core/freyja/demix/environment.yml +++ b/modules/nf-core/freyja/demix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/freyja/update/environment.yml b/modules/nf-core/freyja/update/environment.yml index 69da13f76f3..0b5b6b06f37 100644 --- a/modules/nf-core/freyja/update/environment.yml +++ b/modules/nf-core/freyja/update/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/freyja/variants/environment.yml b/modules/nf-core/freyja/variants/environment.yml index 69da13f76f3..0b5b6b06f37 100644 --- a/modules/nf-core/freyja/variants/environment.yml +++ b/modules/nf-core/freyja/variants/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/galah/environment.yml b/modules/nf-core/galah/environment.yml index d3b58cd5b45..3fa9c851e45 100644 --- a/modules/nf-core/galah/environment.yml +++ b/modules/nf-core/galah/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gamma/gamma/environment.yml b/modules/nf-core/gamma/gamma/environment.yml index a6672129c76..a118a167afd 100644 --- a/modules/nf-core/gamma/gamma/environment.yml +++ b/modules/nf-core/gamma/gamma/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gangstr/environment.yml b/modules/nf-core/gangstr/environment.yml index 9d6bce21a1a..37a6b8e5e43 100644 --- a/modules/nf-core/gangstr/environment.yml +++ b/modules/nf-core/gangstr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ganon/buildcustom/environment.yml b/modules/nf-core/ganon/buildcustom/environment.yml index 0e073d5ba75..002d6630d7d 100644 --- a/modules/nf-core/ganon/buildcustom/environment.yml +++ b/modules/nf-core/ganon/buildcustom/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ganon/classify/environment.yml b/modules/nf-core/ganon/classify/environment.yml index 0e073d5ba75..002d6630d7d 100644 --- a/modules/nf-core/ganon/classify/environment.yml +++ b/modules/nf-core/ganon/classify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ganon/report/environment.yml b/modules/nf-core/ganon/report/environment.yml index 0e073d5ba75..002d6630d7d 100644 --- a/modules/nf-core/ganon/report/environment.yml +++ b/modules/nf-core/ganon/report/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ganon/table/environment.yml b/modules/nf-core/ganon/table/environment.yml index 0e073d5ba75..002d6630d7d 100644 --- a/modules/nf-core/ganon/table/environment.yml +++ b/modules/nf-core/ganon/table/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gappa/examineassign/environment.yml b/modules/nf-core/gappa/examineassign/environment.yml index 0059e1a4997..613698aac98 100644 --- a/modules/nf-core/gappa/examineassign/environment.yml +++ b/modules/nf-core/gappa/examineassign/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gappa/examinegraft/environment.yml b/modules/nf-core/gappa/examinegraft/environment.yml index 0059e1a4997..613698aac98 100644 --- a/modules/nf-core/gappa/examinegraft/environment.yml +++ b/modules/nf-core/gappa/examinegraft/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gappa/examineheattree/environment.yml b/modules/nf-core/gappa/examineheattree/environment.yml index 0059e1a4997..613698aac98 100644 --- a/modules/nf-core/gappa/examineheattree/environment.yml +++ b/modules/nf-core/gappa/examineheattree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk/indelrealigner/environment.yml b/modules/nf-core/gatk/indelrealigner/environment.yml index 6a147cb0866..5cc5246253f 100644 --- a/modules/nf-core/gatk/indelrealigner/environment.yml +++ b/modules/nf-core/gatk/indelrealigner/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk/realignertargetcreator/environment.yml b/modules/nf-core/gatk/realignertargetcreator/environment.yml index 6a147cb0866..5cc5246253f 100644 --- a/modules/nf-core/gatk/realignertargetcreator/environment.yml +++ b/modules/nf-core/gatk/realignertargetcreator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk/unifiedgenotyper/environment.yml b/modules/nf-core/gatk/unifiedgenotyper/environment.yml index 182579ab24e..3f7817afce6 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/environment.yml +++ b/modules/nf-core/gatk/unifiedgenotyper/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::gatk=3.5 - - bioconda::tabix=1.11 ## Needed for bgzip + - bioconda::tabix=1.11 diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index ec65c32da48..8afaba06562 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -7,9 +7,6 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 - # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.19.1 - # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 1f7d0824620..b562b72c740 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml index d04a469c944..b562b72c740 100644 --- a/modules/nf-core/gatk4/variantstotable/environment.yml +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: @@ -7,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/gatk4 - bioconda::gatk4=4.6.1.0 - # renovate: datasource=conda depName=bioconda/gcnvkernel - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index d3e954cdacc..a5c49e95576 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index d3e954cdacc..a5c49e95576 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index d3e954cdacc..a5c49e95576 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 315f6dc67e2..f52109e83b3 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gecco/run/environment.yml b/modules/nf-core/gecco/run/environment.yml index 7db7dc87b41..bb47bc857e2 100644 --- a/modules/nf-core/gecco/run/environment.yml +++ b/modules/nf-core/gecco/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gem2/gem2bedmappability/environment.yml b/modules/nf-core/gem2/gem2bedmappability/environment.yml index bf74e3f0e30..f8d5958a980 100644 --- a/modules/nf-core/gem2/gem2bedmappability/environment.yml +++ b/modules/nf-core/gem2/gem2bedmappability/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gem2/gemindexer/environment.yml b/modules/nf-core/gem2/gemindexer/environment.yml index bf74e3f0e30..f8d5958a980 100644 --- a/modules/nf-core/gem2/gemindexer/environment.yml +++ b/modules/nf-core/gem2/gemindexer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gem2/gemmappability/environment.yml b/modules/nf-core/gem2/gemmappability/environment.yml index bf74e3f0e30..f8d5958a980 100644 --- a/modules/nf-core/gem2/gemmappability/environment.yml +++ b/modules/nf-core/gem2/gemmappability/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gem3/gem3indexer/environment.yml b/modules/nf-core/gem3/gem3indexer/environment.yml index f9e5bd2c188..8eb1364919a 100644 --- a/modules/nf-core/gem3/gem3indexer/environment.yml +++ b/modules/nf-core/gem3/gem3indexer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gem3/gem3mapper/environment.yml b/modules/nf-core/gem3/gem3mapper/environment.yml index 3915ff10611..40f67010df1 100644 --- a/modules/nf-core/gem3/gem3mapper/environment.yml +++ b/modules/nf-core/gem3/gem3mapper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genescopefk/environment.yml b/modules/nf-core/genescopefk/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/genescopefk/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/genmap/index/environment.yml b/modules/nf-core/genmap/index/environment.yml index f54626e43ba..9d97c535562 100644 --- a/modules/nf-core/genmap/index/environment.yml +++ b/modules/nf-core/genmap/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genmap/map/environment.yml b/modules/nf-core/genmap/map/environment.yml index f54626e43ba..9d97c535562 100644 --- a/modules/nf-core/genmap/map/environment.yml +++ b/modules/nf-core/genmap/map/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml index 227ee89204f..163ddf09311 100644 --- a/modules/nf-core/genmod/annotate/environment.yml +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml index 227ee89204f..163ddf09311 100644 --- a/modules/nf-core/genmod/compound/environment.yml +++ b/modules/nf-core/genmod/compound/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml index 227ee89204f..163ddf09311 100644 --- a/modules/nf-core/genmod/models/environment.yml +++ b/modules/nf-core/genmod/models/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml index 227ee89204f..163ddf09311 100644 --- a/modules/nf-core/genmod/score/environment.yml +++ b/modules/nf-core/genmod/score/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genomad/download/environment.yml b/modules/nf-core/genomad/download/environment.yml index 443789ef226..2592afc9143 100644 --- a/modules/nf-core/genomad/download/environment.yml +++ b/modules/nf-core/genomad/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genomad/endtoend/environment.yml b/modules/nf-core/genomad/endtoend/environment.yml index 443789ef226..2592afc9143 100644 --- a/modules/nf-core/genomad/endtoend/environment.yml +++ b/modules/nf-core/genomad/endtoend/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genomescope2/environment.yml b/modules/nf-core/genomescope2/environment.yml index 2b48c6d9ca0..7aabfef166c 100644 --- a/modules/nf-core/genomescope2/environment.yml +++ b/modules/nf-core/genomescope2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genotyphi/parse/environment.yml b/modules/nf-core/genotyphi/parse/environment.yml index a8ca10817aa..376709f088b 100644 --- a/modules/nf-core/genotyphi/parse/environment.yml +++ b/modules/nf-core/genotyphi/parse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/genrich/environment.yml b/modules/nf-core/genrich/environment.yml index cef503551e9..ca55b36c0b2 100644 --- a/modules/nf-core/genrich/environment.yml +++ b/modules/nf-core/genrich/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/geofetch/environment.yml b/modules/nf-core/geofetch/environment.yml index e22890b0929..7aaeb94647a 100644 --- a/modules/nf-core/geofetch/environment.yml +++ b/modules/nf-core/geofetch/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::geofetch=0.12.6" + - bioconda::geofetch=0.12.6 diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml index 3d4f8cd9849..8fff8aceda6 100644 --- a/modules/nf-core/geoquery/getgeo/environment.yml +++ b/modules/nf-core/geoquery/getgeo/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-geoquery=2.70.0 - - conda-forge::r-base=4.3.2 # Locked with container + - conda-forge::r-base=4.3.2 diff --git a/modules/nf-core/gfaffix/environment.yml b/modules/nf-core/gfaffix/environment.yml index 3da9f04984a..da0b2c36684 100644 --- a/modules/nf-core/gfaffix/environment.yml +++ b/modules/nf-core/gfaffix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml index b47bbdbbaf9..cbc93d6105e 100644 --- a/modules/nf-core/gfastats/environment.yml +++ b/modules/nf-core/gfastats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gfatools/gfa2fa/environment.yml b/modules/nf-core/gfatools/gfa2fa/environment.yml index 476a4fcf2ac..b5097cda998 100644 --- a/modules/nf-core/gfatools/gfa2fa/environment.yml +++ b/modules/nf-core/gfatools/gfa2fa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gfatools/stat/environment.yml b/modules/nf-core/gfatools/stat/environment.yml index 476a4fcf2ac..b5097cda998 100644 --- a/modules/nf-core/gfatools/stat/environment.yml +++ b/modules/nf-core/gfatools/stat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gffcompare/environment.yml b/modules/nf-core/gffcompare/environment.yml index 2b52417df44..03b22ea387f 100644 --- a/modules/nf-core/gffcompare/environment.yml +++ b/modules/nf-core/gffcompare/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index ee2398416cf..46c5faecece 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gget/gget/environment.yml b/modules/nf-core/gget/gget/environment.yml index f8dae7c70b2..58e4455858b 100644 --- a/modules/nf-core/gget/gget/environment.yml +++ b/modules/nf-core/gget/gget/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse/chunk/environment.yml b/modules/nf-core/glimpse/chunk/environment.yml index 6247794bdd5..56d614d537e 100644 --- a/modules/nf-core/glimpse/chunk/environment.yml +++ b/modules/nf-core/glimpse/chunk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse/concordance/environment.yml b/modules/nf-core/glimpse/concordance/environment.yml index 6247794bdd5..56d614d537e 100644 --- a/modules/nf-core/glimpse/concordance/environment.yml +++ b/modules/nf-core/glimpse/concordance/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse/ligate/environment.yml b/modules/nf-core/glimpse/ligate/environment.yml index 6247794bdd5..56d614d537e 100644 --- a/modules/nf-core/glimpse/ligate/environment.yml +++ b/modules/nf-core/glimpse/ligate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse/phase/environment.yml b/modules/nf-core/glimpse/phase/environment.yml index 6247794bdd5..56d614d537e 100644 --- a/modules/nf-core/glimpse/phase/environment.yml +++ b/modules/nf-core/glimpse/phase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse/sample/environment.yml b/modules/nf-core/glimpse/sample/environment.yml index 6247794bdd5..56d614d537e 100644 --- a/modules/nf-core/glimpse/sample/environment.yml +++ b/modules/nf-core/glimpse/sample/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse2/chunk/environment.yml b/modules/nf-core/glimpse2/chunk/environment.yml index 75b862396ef..c09fbe3e307 100644 --- a/modules/nf-core/glimpse2/chunk/environment.yml +++ b/modules/nf-core/glimpse2/chunk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse2/concordance/environment.yml b/modules/nf-core/glimpse2/concordance/environment.yml index 75b862396ef..c09fbe3e307 100644 --- a/modules/nf-core/glimpse2/concordance/environment.yml +++ b/modules/nf-core/glimpse2/concordance/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse2/ligate/environment.yml b/modules/nf-core/glimpse2/ligate/environment.yml index 75b862396ef..c09fbe3e307 100644 --- a/modules/nf-core/glimpse2/ligate/environment.yml +++ b/modules/nf-core/glimpse2/ligate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse2/phase/environment.yml b/modules/nf-core/glimpse2/phase/environment.yml index 75b862396ef..c09fbe3e307 100644 --- a/modules/nf-core/glimpse2/phase/environment.yml +++ b/modules/nf-core/glimpse2/phase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glimpse2/splitreference/environment.yml b/modules/nf-core/glimpse2/splitreference/environment.yml index 75b862396ef..c09fbe3e307 100644 --- a/modules/nf-core/glimpse2/splitreference/environment.yml +++ b/modules/nf-core/glimpse2/splitreference/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/glnexus/environment.yml b/modules/nf-core/glnexus/environment.yml index 9190508a96f..b3499146b7b 100644 --- a/modules/nf-core/glnexus/environment.yml +++ b/modules/nf-core/glnexus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gmmdemux/environment.yml b/modules/nf-core/gmmdemux/environment.yml index d8580796f2f..1ddb2fa2a89 100644 --- a/modules/nf-core/gmmdemux/environment.yml +++ b/modules/nf-core/gmmdemux/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::gmm-demux=0.2.2.3" + - bioconda::gmm-demux=0.2.2.3 diff --git a/modules/nf-core/goat/taxonsearch/environment.yml b/modules/nf-core/goat/taxonsearch/environment.yml index e09c2a19b21..a59ddd3ec0f 100644 --- a/modules/nf-core/goat/taxonsearch/environment.yml +++ b/modules/nf-core/goat/taxonsearch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/goleft/indexcov/environment.yml b/modules/nf-core/goleft/indexcov/environment.yml index 813146929cb..7aa46cc4f0d 100644 --- a/modules/nf-core/goleft/indexcov/environment.yml +++ b/modules/nf-core/goleft/indexcov/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/goleft/indexsplit/environment.yml b/modules/nf-core/goleft/indexsplit/environment.yml index 127c0c7a52b..9f185dc303a 100644 --- a/modules/nf-core/goleft/indexsplit/environment.yml +++ b/modules/nf-core/goleft/indexsplit/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gprofiler2/gost/environment.yml b/modules/nf-core/gprofiler2/gost/environment.yml index 14376015da8..6032301de60 100644 --- a/modules/nf-core/gprofiler2/gost/environment.yml +++ b/modules/nf-core/gprofiler2/gost/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/grabix/check/environment.yml b/modules/nf-core/grabix/check/environment.yml index 58787b9b4d2..34ab2c0d315 100644 --- a/modules/nf-core/grabix/check/environment.yml +++ b/modules/nf-core/grabix/check/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/graphmap2/align/environment.yml b/modules/nf-core/graphmap2/align/environment.yml index 2138c7f46a4..2b41d5dc850 100644 --- a/modules/nf-core/graphmap2/align/environment.yml +++ b/modules/nf-core/graphmap2/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/graphmap2/index/environment.yml b/modules/nf-core/graphmap2/index/environment.yml index 2138c7f46a4..2b41d5dc850 100644 --- a/modules/nf-core/graphmap2/index/environment.yml +++ b/modules/nf-core/graphmap2/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/graphtyper/genotype/environment.yml b/modules/nf-core/graphtyper/genotype/environment.yml index 57b5ac801cf..2582ef08aee 100644 --- a/modules/nf-core/graphtyper/genotype/environment.yml +++ b/modules/nf-core/graphtyper/genotype/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml index 57b5ac801cf..2582ef08aee 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gridss/generateponbedpe/environment.yml b/modules/nf-core/gridss/generateponbedpe/environment.yml index db37d675e60..82d2d2f8bbe 100644 --- a/modules/nf-core/gridss/generateponbedpe/environment.yml +++ b/modules/nf-core/gridss/generateponbedpe/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gridss/gridss/environment.yml b/modules/nf-core/gridss/gridss/environment.yml index db37d675e60..82d2d2f8bbe 100644 --- a/modules/nf-core/gridss/gridss/environment.yml +++ b/modules/nf-core/gridss/gridss/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gridss/somaticfilter/environment.yml b/modules/nf-core/gridss/somaticfilter/environment.yml index db37d675e60..82d2d2f8bbe 100644 --- a/modules/nf-core/gridss/somaticfilter/environment.yml +++ b/modules/nf-core/gridss/somaticfilter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gsea/gsea/environment.yml b/modules/nf-core/gsea/gsea/environment.yml index c5780466ab4..c5902557993 100644 --- a/modules/nf-core/gsea/gsea/environment.yml +++ b/modules/nf-core/gsea/gsea/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gstama/collapse/environment.yml b/modules/nf-core/gstama/collapse/environment.yml index cef33450cda..46813d00f79 100644 --- a/modules/nf-core/gstama/collapse/environment.yml +++ b/modules/nf-core/gstama/collapse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gstama/merge/environment.yml b/modules/nf-core/gstama/merge/environment.yml index cef33450cda..46813d00f79 100644 --- a/modules/nf-core/gstama/merge/environment.yml +++ b/modules/nf-core/gstama/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gstama/polyacleanup/environment.yml b/modules/nf-core/gstama/polyacleanup/environment.yml index cef33450cda..46813d00f79 100644 --- a/modules/nf-core/gstama/polyacleanup/environment.yml +++ b/modules/nf-core/gstama/polyacleanup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gt/gff3/environment.yml b/modules/nf-core/gt/gff3/environment.yml index 666eb47f116..0e0154300bd 100644 --- a/modules/nf-core/gt/gff3/environment.yml +++ b/modules/nf-core/gt/gff3/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::genometools-genometools=1.6.5" + - bioconda::genometools-genometools=1.6.5 diff --git a/modules/nf-core/gt/gff3validator/environment.yml b/modules/nf-core/gt/gff3validator/environment.yml index 666eb47f116..0e0154300bd 100644 --- a/modules/nf-core/gt/gff3validator/environment.yml +++ b/modules/nf-core/gt/gff3validator/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::genometools-genometools=1.6.5" + - bioconda::genometools-genometools=1.6.5 diff --git a/modules/nf-core/gt/ltrharvest/environment.yml b/modules/nf-core/gt/ltrharvest/environment.yml index 666eb47f116..0e0154300bd 100644 --- a/modules/nf-core/gt/ltrharvest/environment.yml +++ b/modules/nf-core/gt/ltrharvest/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::genometools-genometools=1.6.5" + - bioconda::genometools-genometools=1.6.5 diff --git a/modules/nf-core/gt/stat/environment.yml b/modules/nf-core/gt/stat/environment.yml index 666eb47f116..0e0154300bd 100644 --- a/modules/nf-core/gt/stat/environment.yml +++ b/modules/nf-core/gt/stat/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::genometools-genometools=1.6.5" + - bioconda::genometools-genometools=1.6.5 diff --git a/modules/nf-core/gt/suffixerator/environment.yml b/modules/nf-core/gt/suffixerator/environment.yml index 666eb47f116..0e0154300bd 100644 --- a/modules/nf-core/gt/suffixerator/environment.yml +++ b/modules/nf-core/gt/suffixerator/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::genometools-genometools=1.6.5" + - bioconda::genometools-genometools=1.6.5 diff --git a/modules/nf-core/gtdbtk/classifywf/environment.yml b/modules/nf-core/gtdbtk/classifywf/environment.yml index 500531eadc7..f0b4a7504b8 100644 --- a/modules/nf-core/gtdbtk/classifywf/environment.yml +++ b/modules/nf-core/gtdbtk/classifywf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gtfsort/environment.yml b/modules/nf-core/gtfsort/environment.yml index 34753e4dd2c..a78b2ef9d9f 100644 --- a/modules/nf-core/gtfsort/environment.yml +++ b/modules/nf-core/gtfsort/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::gtfsort=0.2.2" + - bioconda::gtfsort=0.2.2 diff --git a/modules/nf-core/gubbins/environment.yml b/modules/nf-core/gubbins/environment.yml index 25ae21c0058..942f0fb4468 100644 --- a/modules/nf-core/gubbins/environment.yml +++ b/modules/nf-core/gubbins/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunc/downloaddb/environment.yml b/modules/nf-core/gunc/downloaddb/environment.yml index 3a0264f4371..c757c1fd544 100644 --- a/modules/nf-core/gunc/downloaddb/environment.yml +++ b/modules/nf-core/gunc/downloaddb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunc/mergecheckm/environment.yml b/modules/nf-core/gunc/mergecheckm/environment.yml index 3a0264f4371..c757c1fd544 100644 --- a/modules/nf-core/gunc/mergecheckm/environment.yml +++ b/modules/nf-core/gunc/mergecheckm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunc/run/environment.yml b/modules/nf-core/gunc/run/environment.yml index 3a0264f4371..c757c1fd544 100644 --- a/modules/nf-core/gunc/run/environment.yml +++ b/modules/nf-core/gunc/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gvcftools/extractvariants/environment.yml b/modules/nf-core/gvcftools/extractvariants/environment.yml index ebe01104141..c8716e57b09 100644 --- a/modules/nf-core/gvcftools/extractvariants/environment.yml +++ b/modules/nf-core/gvcftools/extractvariants/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gzrt/environment.yml b/modules/nf-core/gzrt/environment.yml index 92cec669a77..5627444f2c2 100644 --- a/modules/nf-core/gzrt/environment.yml +++ b/modules/nf-core/gzrt/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::gzrt=0.9.1" + - bioconda::gzrt=0.9.1 diff --git a/modules/nf-core/hamronization/abricate/environment.yml b/modules/nf-core/hamronization/abricate/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/abricate/environment.yml +++ b/modules/nf-core/hamronization/abricate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/amrfinderplus/environment.yml b/modules/nf-core/hamronization/amrfinderplus/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/amrfinderplus/environment.yml +++ b/modules/nf-core/hamronization/amrfinderplus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/deeparg/environment.yml b/modules/nf-core/hamronization/deeparg/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/deeparg/environment.yml +++ b/modules/nf-core/hamronization/deeparg/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/fargene/environment.yml b/modules/nf-core/hamronization/fargene/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/fargene/environment.yml +++ b/modules/nf-core/hamronization/fargene/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/rgi/environment.yml b/modules/nf-core/hamronization/rgi/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/rgi/environment.yml +++ b/modules/nf-core/hamronization/rgi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hamronization/summarize/environment.yml b/modules/nf-core/hamronization/summarize/environment.yml index 791b9c96108..5826a865538 100644 --- a/modules/nf-core/hamronization/summarize/environment.yml +++ b/modules/nf-core/hamronization/summarize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hapibd/environment.yml b/modules/nf-core/hapibd/environment.yml index 0e4cf39fb4b..8da5920c7d7 100644 --- a/modules/nf-core/hapibd/environment.yml +++ b/modules/nf-core/hapibd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml index 4fb40238b7d..d74b4d7eda1 100644 --- a/modules/nf-core/haplocheck/environment.yml +++ b/modules/nf-core/haplocheck/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/haplogrep2/classify/environment.yml b/modules/nf-core/haplogrep2/classify/environment.yml index b84579e6747..756022e7b3a 100644 --- a/modules/nf-core/haplogrep2/classify/environment.yml +++ b/modules/nf-core/haplogrep2/classify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/haplogrep3/classify/environment.yml b/modules/nf-core/haplogrep3/classify/environment.yml index ca0c7e6919a..c219ac43c3b 100644 --- a/modules/nf-core/haplogrep3/classify/environment.yml +++ b/modules/nf-core/haplogrep3/classify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/happy/ftxpy/environment.yml b/modules/nf-core/happy/ftxpy/environment.yml index cc251479f64..3ffc3369eac 100644 --- a/modules/nf-core/happy/ftxpy/environment.yml +++ b/modules/nf-core/happy/ftxpy/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::hap.py=0.3.15" + - bioconda::hap.py=0.3.15 diff --git a/modules/nf-core/happy/happy/environment.yml b/modules/nf-core/happy/happy/environment.yml index d65fa5db90a..d1c22b5e7e9 100644 --- a/modules/nf-core/happy/happy/environment.yml +++ b/modules/nf-core/happy/happy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/happy/prepy/environment.yml b/modules/nf-core/happy/prepy/environment.yml index d65fa5db90a..d1c22b5e7e9 100644 --- a/modules/nf-core/happy/prepy/environment.yml +++ b/modules/nf-core/happy/prepy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/happy/sompy/environment.yml b/modules/nf-core/happy/sompy/environment.yml index d65fa5db90a..d1c22b5e7e9 100644 --- a/modules/nf-core/happy/sompy/environment.yml +++ b/modules/nf-core/happy/sompy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hicap/environment.yml b/modules/nf-core/hicap/environment.yml index 6eb0186fd8d..540f77b1353 100644 --- a/modules/nf-core/hicap/environment.yml +++ b/modules/nf-core/hicap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hicexplorer/hicpca/environment.yml b/modules/nf-core/hicexplorer/hicpca/environment.yml index 4b8b663fb7a..758410eb28a 100644 --- a/modules/nf-core/hicexplorer/hicpca/environment.yml +++ b/modules/nf-core/hicexplorer/hicpca/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml index 6aea679a78f..b7ba1981a62 100644 --- a/modules/nf-core/hifiasm/environment.yml +++ b/modules/nf-core/hifiasm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hiphase/environment.yml b/modules/nf-core/hiphase/environment.yml index 90f9823f0a7..f0ee56e0472 100644 --- a/modules/nf-core/hiphase/environment.yml +++ b/modules/nf-core/hiphase/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::hiphase=1.4.5" + - bioconda::hiphase=1.4.5 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 26c62a3bfda..804be5ef839 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index afced73382d..246a78af32e 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index afced73382d..246a78af32e 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hlala/preparegraph/environment.yml b/modules/nf-core/hlala/preparegraph/environment.yml index 3cebeff05bf..029d7a4a21a 100644 --- a/modules/nf-core/hlala/preparegraph/environment.yml +++ b/modules/nf-core/hlala/preparegraph/environment.yml @@ -1,3 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda +dependencies: + - bioconda::hla-la=1.0.4 diff --git a/modules/nf-core/hlala/typing/environment.yml b/modules/nf-core/hlala/typing/environment.yml index 00695d60827..e1383b84a99 100644 --- a/modules/nf-core/hlala/typing/environment.yml +++ b/modules/nf-core/hlala/typing/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmcopy/gccounter/environment.yml b/modules/nf-core/hmmcopy/gccounter/environment.yml index 8284f1c2095..77e6904f404 100644 --- a/modules/nf-core/hmmcopy/gccounter/environment.yml +++ b/modules/nf-core/hmmcopy/gccounter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmcopy/generatemap/environment.yml b/modules/nf-core/hmmcopy/generatemap/environment.yml index 8284f1c2095..77e6904f404 100644 --- a/modules/nf-core/hmmcopy/generatemap/environment.yml +++ b/modules/nf-core/hmmcopy/generatemap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmcopy/mapcounter/environment.yml b/modules/nf-core/hmmcopy/mapcounter/environment.yml index 8284f1c2095..77e6904f404 100644 --- a/modules/nf-core/hmmcopy/mapcounter/environment.yml +++ b/modules/nf-core/hmmcopy/mapcounter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmcopy/readcounter/environment.yml b/modules/nf-core/hmmcopy/readcounter/environment.yml index 8284f1c2095..77e6904f404 100644 --- a/modules/nf-core/hmmcopy/readcounter/environment.yml +++ b/modules/nf-core/hmmcopy/readcounter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/eslalimask/environment.yml b/modules/nf-core/hmmer/eslalimask/environment.yml index 7c62eac7e3a..83d20a9294c 100644 --- a/modules/nf-core/hmmer/eslalimask/environment.yml +++ b/modules/nf-core/hmmer/eslalimask/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/eslreformat/environment.yml b/modules/nf-core/hmmer/eslreformat/environment.yml index 7c62eac7e3a..83d20a9294c 100644 --- a/modules/nf-core/hmmer/eslreformat/environment.yml +++ b/modules/nf-core/hmmer/eslreformat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmalign/environment.yml b/modules/nf-core/hmmer/hmmalign/environment.yml index c5ddec5d912..1967d405f55 100644 --- a/modules/nf-core/hmmer/hmmalign/environment.yml +++ b/modules/nf-core/hmmer/hmmalign/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmbuild/environment.yml b/modules/nf-core/hmmer/hmmbuild/environment.yml index c5ddec5d912..1967d405f55 100644 --- a/modules/nf-core/hmmer/hmmbuild/environment.yml +++ b/modules/nf-core/hmmer/hmmbuild/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmfetch/environment.yml b/modules/nf-core/hmmer/hmmfetch/environment.yml index 7c62eac7e3a..83d20a9294c 100644 --- a/modules/nf-core/hmmer/hmmfetch/environment.yml +++ b/modules/nf-core/hmmer/hmmfetch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmrank/environment.yml b/modules/nf-core/hmmer/hmmrank/environment.yml index fbce96e2508..dfc0f14b4c4 100644 --- a/modules/nf-core/hmmer/hmmrank/environment.yml +++ b/modules/nf-core/hmmer/hmmrank/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmsearch/environment.yml b/modules/nf-core/hmmer/hmmsearch/environment.yml index c5ddec5d912..1967d405f55 100644 --- a/modules/nf-core/hmmer/hmmsearch/environment.yml +++ b/modules/nf-core/hmmer/hmmsearch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmtnote/annotate/environment.yml b/modules/nf-core/hmtnote/annotate/environment.yml index 1d9d20e3fe9..2e3e148943e 100644 --- a/modules/nf-core/hmtnote/annotate/environment.yml +++ b/modules/nf-core/hmtnote/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/homer/annotatepeaks/environment.yml b/modules/nf-core/homer/annotatepeaks/environment.yml index 05b3acf2661..3a556e4c9f9 100644 --- a/modules/nf-core/homer/annotatepeaks/environment.yml +++ b/modules/nf-core/homer/annotatepeaks/environment.yml @@ -1,10 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-deseq2=1.42.0 - bioconda::bioconductor-edger=4.0.16 - # renovate: datasource=conda depName=bioconda/homer - bioconda::homer=4.11 - bioconda::samtools=1.21 - conda-forge::r-essentials=4.3 diff --git a/modules/nf-core/homer/findpeaks/environment.yml b/modules/nf-core/homer/findpeaks/environment.yml index 05b3acf2661..3a556e4c9f9 100644 --- a/modules/nf-core/homer/findpeaks/environment.yml +++ b/modules/nf-core/homer/findpeaks/environment.yml @@ -1,10 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-deseq2=1.42.0 - bioconda::bioconductor-edger=4.0.16 - # renovate: datasource=conda depName=bioconda/homer - bioconda::homer=4.11 - bioconda::samtools=1.21 - conda-forge::r-essentials=4.3 diff --git a/modules/nf-core/homer/maketagdirectory/environment.yml b/modules/nf-core/homer/maketagdirectory/environment.yml index 05b3acf2661..3a556e4c9f9 100644 --- a/modules/nf-core/homer/maketagdirectory/environment.yml +++ b/modules/nf-core/homer/maketagdirectory/environment.yml @@ -1,10 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-deseq2=1.42.0 - bioconda::bioconductor-edger=4.0.16 - # renovate: datasource=conda depName=bioconda/homer - bioconda::homer=4.11 - bioconda::samtools=1.21 - conda-forge::r-essentials=4.3 diff --git a/modules/nf-core/homer/makeucscfile/environment.yml b/modules/nf-core/homer/makeucscfile/environment.yml index 05b3acf2661..3a556e4c9f9 100644 --- a/modules/nf-core/homer/makeucscfile/environment.yml +++ b/modules/nf-core/homer/makeucscfile/environment.yml @@ -1,10 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-deseq2=1.42.0 - bioconda::bioconductor-edger=4.0.16 - # renovate: datasource=conda depName=bioconda/homer - bioconda::homer=4.11 - bioconda::samtools=1.21 - conda-forge::r-essentials=4.3 diff --git a/modules/nf-core/homer/pos2bed/environment.yml b/modules/nf-core/homer/pos2bed/environment.yml index 05b3acf2661..3a556e4c9f9 100644 --- a/modules/nf-core/homer/pos2bed/environment.yml +++ b/modules/nf-core/homer/pos2bed/environment.yml @@ -1,10 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::bioconductor-deseq2=1.42.0 - bioconda::bioconductor-edger=4.0.16 - # renovate: datasource=conda depName=bioconda/homer - bioconda::homer=4.11 - bioconda::samtools=1.21 - conda-forge::r-essentials=4.3 diff --git a/modules/nf-core/hostile/fetch/environment.yml b/modules/nf-core/hostile/fetch/environment.yml index ef103e9a834..17994cbcedf 100644 --- a/modules/nf-core/hostile/fetch/environment.yml +++ b/modules/nf-core/hostile/fetch/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::hostile=1.1.0" + - bioconda::hostile=1.1.0 diff --git a/modules/nf-core/hpsuissero/environment.yml b/modules/nf-core/hpsuissero/environment.yml index 000ffe9112b..50fd1f7cf39 100644 --- a/modules/nf-core/hpsuissero/environment.yml +++ b/modules/nf-core/hpsuissero/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/htseq/count/environment.yml b/modules/nf-core/htseq/count/environment.yml index f1f6a7f0cc8..cfb7970f5b1 100644 --- a/modules/nf-core/htseq/count/environment.yml +++ b/modules/nf-core/htseq/count/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/htsnimtools/vcfcheck/environment.yml b/modules/nf-core/htsnimtools/vcfcheck/environment.yml index 1129a644718..d7b6646300d 100644 --- a/modules/nf-core/htsnimtools/vcfcheck/environment.yml +++ b/modules/nf-core/htsnimtools/vcfcheck/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::hts-nim-tools=0.3.11" + - bioconda::hts-nim-tools=0.3.11 diff --git a/modules/nf-core/humid/environment.yml b/modules/nf-core/humid/environment.yml index b5e4a814c42..94e523bc64b 100644 --- a/modules/nf-core/humid/environment.yml +++ b/modules/nf-core/humid/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::humid=1.0.4" + - bioconda::humid=1.0.4 diff --git a/modules/nf-core/hypo/environment.yml b/modules/nf-core/hypo/environment.yml index 9182668f41f..0e6ecc40c9b 100644 --- a/modules/nf-core/hypo/environment.yml +++ b/modules/nf-core/hypo/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ichorcna/createpon/environment.yml b/modules/nf-core/ichorcna/createpon/environment.yml index a676ae360e3..54df91b4f29 100644 --- a/modules/nf-core/ichorcna/createpon/environment.yml +++ b/modules/nf-core/ichorcna/createpon/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ichorcna/run/environment.yml b/modules/nf-core/ichorcna/run/environment.yml index a676ae360e3..54df91b4f29 100644 --- a/modules/nf-core/ichorcna/run/environment.yml +++ b/modules/nf-core/ichorcna/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/icountmini/metagene/environment.yml b/modules/nf-core/icountmini/metagene/environment.yml index d1ebc705ec0..16acb3d0e32 100644 --- a/modules/nf-core/icountmini/metagene/environment.yml +++ b/modules/nf-core/icountmini/metagene/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/icountmini/peaks/environment.yml b/modules/nf-core/icountmini/peaks/environment.yml index 02e0549f55c..5aa916c11ea 100644 --- a/modules/nf-core/icountmini/peaks/environment.yml +++ b/modules/nf-core/icountmini/peaks/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/icountmini/segment/environment.yml b/modules/nf-core/icountmini/segment/environment.yml index 02e0549f55c..5aa916c11ea 100644 --- a/modules/nf-core/icountmini/segment/environment.yml +++ b/modules/nf-core/icountmini/segment/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/icountmini/sigxls/environment.yml b/modules/nf-core/icountmini/sigxls/environment.yml index 02e0549f55c..5aa916c11ea 100644 --- a/modules/nf-core/icountmini/sigxls/environment.yml +++ b/modules/nf-core/icountmini/sigxls/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/icountmini/summary/environment.yml b/modules/nf-core/icountmini/summary/environment.yml index 02e0549f55c..5aa916c11ea 100644 --- a/modules/nf-core/icountmini/summary/environment.yml +++ b/modules/nf-core/icountmini/summary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/idemux/environment.yml b/modules/nf-core/idemux/environment.yml index 0ab6c3fa1b2..3839c9f937c 100644 --- a/modules/nf-core/idemux/environment.yml +++ b/modules/nf-core/idemux/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::idemux=0.1.6" + - bioconda::idemux=0.1.6 diff --git a/modules/nf-core/idr/environment.yml b/modules/nf-core/idr/environment.yml index 60af1d2e0b0..81c84ebbf99 100644 --- a/modules/nf-core/idr/environment.yml +++ b/modules/nf-core/idr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/igv/js/environment.yml b/modules/nf-core/igv/js/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/igv/js/environment.yml +++ b/modules/nf-core/igv/js/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/igvreports/environment.yml b/modules/nf-core/igvreports/environment.yml index fc4c39fd65f..915573b3410 100644 --- a/modules/nf-core/igvreports/environment.yml +++ b/modules/nf-core/igvreports/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::igv-reports=1.12.0" + - bioconda::igv-reports=1.12.0 diff --git a/modules/nf-core/ilastik/multicut/environment.yml b/modules/nf-core/ilastik/multicut/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/ilastik/multicut/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/ilastik/pixelclassification/environment.yml b/modules/nf-core/ilastik/pixelclassification/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/ilastik/pixelclassification/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/immunedeconv/environment.yml b/modules/nf-core/immunedeconv/environment.yml index 004fc39bed0..413c48af2de 100644 --- a/modules/nf-core/immunedeconv/environment.yml +++ b/modules/nf-core/immunedeconv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/instrain/compare/environment.yml b/modules/nf-core/instrain/compare/environment.yml index 38edb5dc5ff..cca5e0e2136 100644 --- a/modules/nf-core/instrain/compare/environment.yml +++ b/modules/nf-core/instrain/compare/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::instrain=1.7.1 - - bioconda::samtools=1.16.1 # Version from container + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/instrain/profile/environment.yml b/modules/nf-core/instrain/profile/environment.yml index 38edb5dc5ff..cca5e0e2136 100644 --- a/modules/nf-core/instrain/profile/environment.yml +++ b/modules/nf-core/instrain/profile/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::instrain=1.7.1 - - bioconda::samtools=1.16.1 # Version from container + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/interproscan/environment.yml b/modules/nf-core/interproscan/environment.yml index d1ce2af7927..8e82f0038ae 100644 --- a/modules/nf-core/interproscan/environment.yml +++ b/modules/nf-core/interproscan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/iphop/download/environment.yml b/modules/nf-core/iphop/download/environment.yml index 871100c66a5..4aba7dd51b0 100644 --- a/modules/nf-core/iphop/download/environment.yml +++ b/modules/nf-core/iphop/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/iphop/predict/environment.yml b/modules/nf-core/iphop/predict/environment.yml index 871100c66a5..4aba7dd51b0 100644 --- a/modules/nf-core/iphop/predict/environment.yml +++ b/modules/nf-core/iphop/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/iqtree/environment.yml b/modules/nf-core/iqtree/environment.yml index 702c05086be..ff1f1fb996c 100644 --- a/modules/nf-core/iqtree/environment.yml +++ b/modules/nf-core/iqtree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/irescue/environment.yml b/modules/nf-core/irescue/environment.yml index 30766a63c50..c3f3d7bb5ca 100644 --- a/modules/nf-core/irescue/environment.yml +++ b/modules/nf-core/irescue/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::irescue=1.1.2" + - bioconda::irescue=1.1.2 diff --git a/modules/nf-core/islandpath/environment.yml b/modules/nf-core/islandpath/environment.yml index 71cb9ec6b94..e1898ce5653 100644 --- a/modules/nf-core/islandpath/environment.yml +++ b/modules/nf-core/islandpath/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ismapper/environment.yml b/modules/nf-core/ismapper/environment.yml index 5249a0a86b7..36ce6892d48 100644 --- a/modules/nf-core/ismapper/environment.yml +++ b/modules/nf-core/ismapper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/isoseq/cluster/environment.yml b/modules/nf-core/isoseq/cluster/environment.yml index f048d21c2e1..7be32539b25 100644 --- a/modules/nf-core/isoseq/cluster/environment.yml +++ b/modules/nf-core/isoseq/cluster/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/isoseq/refine/environment.yml b/modules/nf-core/isoseq/refine/environment.yml index f048d21c2e1..7be32539b25 100644 --- a/modules/nf-core/isoseq/refine/environment.yml +++ b/modules/nf-core/isoseq/refine/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/isoseq3/tag/environment.yml b/modules/nf-core/isoseq3/tag/environment.yml index ec4d15e58a8..9f80447cda4 100644 --- a/modules/nf-core/isoseq3/tag/environment.yml +++ b/modules/nf-core/isoseq3/tag/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::isoseq3=4.0.0" + - bioconda::isoseq3=4.0.0 diff --git a/modules/nf-core/ivar/consensus/environment.yml b/modules/nf-core/ivar/consensus/environment.yml index 6d04535789f..e56a6e7cdf4 100644 --- a/modules/nf-core/ivar/consensus/environment.yml +++ b/modules/nf-core/ivar/consensus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ivar/trim/environment.yml b/modules/nf-core/ivar/trim/environment.yml index 6d04535789f..e56a6e7cdf4 100644 --- a/modules/nf-core/ivar/trim/environment.yml +++ b/modules/nf-core/ivar/trim/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ivar/variants/environment.yml b/modules/nf-core/ivar/variants/environment.yml index 6d04535789f..e56a6e7cdf4 100644 --- a/modules/nf-core/ivar/variants/environment.yml +++ b/modules/nf-core/ivar/variants/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/jasminesv/environment.yml b/modules/nf-core/jasminesv/environment.yml index 7a0da03aa06..1f9ff1b5b08 100644 --- a/modules/nf-core/jasminesv/environment.yml +++ b/modules/nf-core/jasminesv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/jasminesv/main.nf b/modules/nf-core/jasminesv/main.nf index 73ad5058978..67721499055 100644 --- a/modules/nf-core/jasminesv/main.nf +++ b/modules/nf-core/jasminesv/main.nf @@ -8,14 +8,14 @@ process JASMINESV { 'biocontainers/jasminesv:1.1.5--hdfd78af_0' }" input: - tuple val(meta), path(vcfs), path(bams), path(sample_dists) + tuple val(meta), path(vcfs, arity:'1..*'), path(bams), path(sample_dists) tuple val(meta2), path(fasta) tuple val(meta3), path(fasta_fai) path(chr_norm) output: - tuple val(meta), path("*.vcf.gz") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz") , emit: vcf + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -26,13 +26,19 @@ process JASMINESV { def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - make_bam = bams ? "ls *.bam > bams.txt" : "" - bam_argument = bams ? "bam_list=bams.txt" : "" - iris_argument = args2 != '' ? "iris_args=${args2}" : "" - sample_dists_argument = sample_dists ? "sample_dists=${sample_dists}" : "" - chr_norm_argument = chr_norm ? "chr_norm_file=${chr_norm}" : "" + def make_bam = bams ? "ls *.bam > bams.txt" : "" + def bam_argument = bams ? "bam_list=bams.txt" : "" + def iris_argument = args2 != '' ? "iris_args=${args2}" : "" + def sample_dists_argument = sample_dists ? "sample_dists=${sample_dists}" : "" + def chr_norm_argument = chr_norm ? "chr_norm_file=${chr_norm}" : "" + + def first_vcf = vcfs[0].name.replaceAll(".gz\$", "") + def unzip_inputs = vcfs.collect { it.name.endsWith(".vcf.gz") ? " bgzip -d --threads ${task.cpus} ${args2} ${it}" : "" }.join("\n") + + vcfs.each { vcf -> + if ("$vcf".startsWith("${prefix}.vcf")) error "Input and output names are the same, set prefix in module configuration to disambiguate!" + } - unzip_inputs = vcfs.collect { it.extension == "gz" ? " bgzip -d --threads ${task.cpus} ${args2} ${it}" : "" }.join("\n") """ ${unzip_inputs} @@ -50,25 +56,35 @@ process JASMINESV { ${chr_norm_argument} \\ ${args} - bgzip --threads ${task.cpus} ${args3} ${prefix}.vcf + if [ -s ${prefix}.vcf ]; then + echo "The file is not empty" + bgzip --threads ${task.cpus} ${args3} ${prefix}.vcf + else + echo "The file is empty, using the header of the first VCF as output file" + cat ${first_vcf} | grep "#" | bgzip --threads ${task.cpus} ${args3} > ${prefix}.vcf.gz + fi cat <<-END_VERSIONS > versions.yml "${task.process}": jasminesv: \$(echo \$(jasmine 2>&1 | grep "version" | sed 's/Jasmine version //')) - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" + vcfs.each { vcf -> + if ("$vcf".startsWith("${prefix}.vcf")) error "Input and output names are the same, set prefix in module configuration to disambiguate!" + } + """ echo "" | gzip > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": jasminesv: \$(echo \$(jasmine 2>&1 | grep "version" | sed 's/Jasmine version //')) - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/jasminesv/tests/iris.config b/modules/nf-core/jasminesv/tests/iris.config deleted file mode 100644 index f61a65bb3cb..00000000000 --- a/modules/nf-core/jasminesv/tests/iris.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: "JASMINESV" { - ext.args = "--run_iris" - ext.args2 = {"threads=1,--pacbio,min_ins_length=30"} - } -} diff --git a/modules/nf-core/jasminesv/tests/main.nf.test b/modules/nf-core/jasminesv/tests/main.nf.test index 851f3383e0a..efb75e6bd77 100644 --- a/modules/nf-core/jasminesv/tests/main.nf.test +++ b/modules/nf-core/jasminesv/tests/main.nf.test @@ -8,7 +8,9 @@ nextflow_process { tag "modules_nfcore" tag "jasminesv" - test("homo_sapiens - [vcf, vcf2], [], [], [], [], []") { + config "./nextflow.config" + + test("homo_sapiens - [vcf, vcf2], [], [], [], [], [] - vcf") { when { process { @@ -32,13 +34,24 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("vcf") } + { assert snapshot( + process.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + // Skip the integer keys + return null + } + if(key == "vcf") { + return [key, val.collect { it.collect { it instanceof Map ? it : path(it).vcf.summary } }] + } + return [key, val] + }.findAll { it != null } + ).match() } ) } } - test("homo_sapiens - [vcf_gz, vcf_gz2], [], [], [], [], []") { + test("homo_sapiens - [vcf_gz, vcf_gz2], [], [], [], [], [] - vcf.gz") { when { process { @@ -62,17 +75,30 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("vcf_gz") } + { assert snapshot( + process.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + // Skip the integer keys + return null + } + if(key == "vcf") { + return [key, val.collect { it.collect { it instanceof Map ? it : path(it).vcf.summary } }] + } + return [key, val] + }.findAll { it != null } + ).match() } ) } } - test("homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, []") { - - config "./iris.config" + test("homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, [] - iris") { when { + params { + args = "--run_iris" + args2 = "threads=1,--pacbio,min_ins_length=30" + } process { """ input[0] = [ @@ -103,17 +129,29 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("iris") } + { assert snapshot( + process.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + // Skip the integer keys + return null + } + if(key == "vcf") { + return [key, val.collect { it.collect { it instanceof Map ? it : path(it).vcf.summary } }] + } + return [key, val] + }.findAll { it != null } + ).match() } ) } } - test("homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, txt") { - - config "./normalize.config" + test("homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, txt - normalize") { when { + params { + args = "--normalize_chrs" + } process { """ input[0] = [ @@ -144,7 +182,18 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("normalize") } + { assert snapshot( + process.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + // Skip the integer keys + return null + } + if(key == "vcf") { + return [key, val.collect { it.collect { it instanceof Map ? it : path(it).vcf.summary } }] + } + return [key, val] + }.findAll { it != null } + ).match() } ) } @@ -176,7 +225,50 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("stub") } + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, vcf2], [], [], [], [], [] - empty vcf - not stub, but linting complains otherwise") { + + when { + params { + args = "min_support=2" + } + process { + """ + input[0] = [ + [ id:"test" ], + [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists:true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/empty.vcf.gz", checkIfExists:true), ], + [], + [] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + // Skip the integer keys + return null + } + if(key == "vcf") { + return [key, val.collect { it.collect { it instanceof Map ? it : path(it).vcf.summary } }] + } + return [key, val] + }.findAll { it != null } + ).match() } ) } diff --git a/modules/nf-core/jasminesv/tests/main.nf.test.snap b/modules/nf-core/jasminesv/tests/main.nf.test.snap index 12032759885..e050316da05 100644 --- a/modules/nf-core/jasminesv/tests/main.nf.test.snap +++ b/modules/nf-core/jasminesv/tests/main.nf.test.snap @@ -1,104 +1,71 @@ { - "iris": { + "homo_sapiens - [vcf, vcf2], [], [], [], [], [] - empty vcf - not stub, but linting complains otherwise": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,4140a44d52426b17c4882a2b4d7508fb" - ] - ], - "1": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" - ], "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,4140a44d52426b17c4882a2b4d7508fb" + "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]" ] ], "versions": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.4" }, - "timestamp": "2024-05-06T11:31:25.797756867" + "timestamp": "2025-02-06T15:10:53.589673221" }, - "vcf_gz": { + "homo_sapiens - [vcf, vcf2], [], [], [], [], [] - vcf": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,aec8e2a90831e84b5e0f8dfa6b80fef5" - ] - ], - "1": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" - ], "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,aec8e2a90831e84b5e0f8dfa6b80fef5" + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=207, phased=false, phasedAutodetect=false]" ] ], "versions": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.4" }, - "timestamp": "2024-05-06T11:31:17.166819477" + "timestamp": "2025-02-06T15:09:35.406672231" }, - "normalize": { + "homo_sapiens - [vcf_gz, vcf_gz2], [], [], [], [], [] - vcf.gz": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,ee57b923cb0a6e2af25790942281fa09" - ] - ], - "1": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" - ], "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,ee57b923cb0a6e2af25790942281fa09" + "VcfFile [chromosomes=[chr21, chr22], sampleCount=1, variantCount=738, phased=false, phasedAutodetect=false]" ] ], "versions": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.4" }, - "timestamp": "2024-05-06T11:31:33.298107095" + "timestamp": "2025-02-06T15:09:42.666253059" }, - "vcf": { + "homo_sapiens - [vcf, vcf2], [], [], [], [], [] - stub": { "content": [ { "0": [ @@ -106,62 +73,73 @@ { "id": "test" }, - "test.vcf.gz:md5,a5f2ea4423010007d26bd61adb169eb7" + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ], "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,a5f2ea4423010007d26bd61adb169eb7" + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.4" }, - "timestamp": "2024-05-06T11:31:09.71125551" + "timestamp": "2025-02-06T13:19:28.224152765" }, - "stub": { + "homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, txt - normalize": { "content": [ { - "0": [ + "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "VcfFile [chromosomes=[22], sampleCount=1, variantCount=207, phased=false, phasedAutodetect=false]" ] ], - "1": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" - ], + "versions": [ + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-06T15:09:58.394068285" + }, + "homo_sapiens - [vcf, vcf2], [bam, bam2], [], fasta, fai, [] - iris": { + "content": [ + { "vcf": [ [ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=205, phased=false, phasedAutodetect=false]" ] ], "versions": [ - "versions.yml:md5,4551c0b18f219ada906fbca1f71e06b0" + "versions.yml:md5,41765be9d926daaf66d9f8cc1ae88820" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.4" }, - "timestamp": "2024-05-06T11:31:41.394853501" + "timestamp": "2025-02-06T15:10:35.020277741" } } \ No newline at end of file diff --git a/modules/nf-core/jasminesv/tests/nextflow.config b/modules/nf-core/jasminesv/tests/nextflow.config new file mode 100644 index 00000000000..3e5851e3d02 --- /dev/null +++ b/modules/nf-core/jasminesv/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + withName: "JASMINESV" { + ext.args = { params.args ?: "" } + ext.args2 = { params.args2 ?: "" } + ext.args3 = { params.args3 ?: "" } + } +} diff --git a/modules/nf-core/jasminesv/tests/normalize.config b/modules/nf-core/jasminesv/tests/normalize.config deleted file mode 100644 index df20a56c741..00000000000 --- a/modules/nf-core/jasminesv/tests/normalize.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: "JASMINESV" { - ext.args = "--normalize_chrs" - } -} diff --git a/modules/nf-core/jupyternotebook/environment.yml b/modules/nf-core/jupyternotebook/environment.yml index a11d11b0c61..354ae3880ad 100644 --- a/modules/nf-core/jupyternotebook/environment.yml +++ b/modules/nf-core/jupyternotebook/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/jvarkit/dict2bed/environment.yml b/modules/nf-core/jvarkit/dict2bed/environment.yml index 14d0e3387c5..5d17d10f64e 100644 --- a/modules/nf-core/jvarkit/dict2bed/environment.yml +++ b/modules/nf-core/jvarkit/dict2bed/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::jvarkit=2024.08.25" + - bioconda::jvarkit=2024.08.25 diff --git a/modules/nf-core/jvarkit/sam2tsv/environment.yml b/modules/nf-core/jvarkit/sam2tsv/environment.yml index 013223af092..7840caa461a 100644 --- a/modules/nf-core/jvarkit/sam2tsv/environment.yml +++ b/modules/nf-core/jvarkit/sam2tsv/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - bioconda - conda-forge dependencies: - - "bioconda::jvarkit=2024.08.25" + - bioconda::jvarkit=2024.08.25 diff --git a/modules/nf-core/jvarkit/vcf2table/environment.yml b/modules/nf-core/jvarkit/vcf2table/environment.yml index 18aee65ed61..ce50e78b490 100644 --- a/modules/nf-core/jvarkit/vcf2table/environment.yml +++ b/modules/nf-core/jvarkit/vcf2table/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda:bcftools=1.20" - - "bioconda::jvarkit=2024.08.25" + - bioconda::jvarkit=2024.08.25 + - bioconda:bcftools=1.20 diff --git a/modules/nf-core/jvarkit/vcffilterjdk/environment.yml b/modules/nf-core/jvarkit/vcffilterjdk/environment.yml index bc395065668..ce50e78b490 100644 --- a/modules/nf-core/jvarkit/vcffilterjdk/environment.yml +++ b/modules/nf-core/jvarkit/vcffilterjdk/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::jvarkit=2024.08.25" - - "bioconda:bcftools=1.20" + - bioconda::jvarkit=2024.08.25 + - bioconda:bcftools=1.20 diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml index e71f3d43668..7840caa461a 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - "bioconda::jvarkit=2024.08.25" + - bioconda::jvarkit=2024.08.25 diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml b/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml index 14d0e3387c5..5d17d10f64e 100644 --- a/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml +++ b/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::jvarkit=2024.08.25" + - bioconda::jvarkit=2024.08.25 diff --git a/modules/nf-core/kaiju/kaiju/environment.yml b/modules/nf-core/kaiju/kaiju/environment.yml index 3bb316c1caf..c095312ac3f 100644 --- a/modules/nf-core/kaiju/kaiju/environment.yml +++ b/modules/nf-core/kaiju/kaiju/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kaiju/kaiju2krona/environment.yml b/modules/nf-core/kaiju/kaiju2krona/environment.yml index 3bb316c1caf..c095312ac3f 100644 --- a/modules/nf-core/kaiju/kaiju2krona/environment.yml +++ b/modules/nf-core/kaiju/kaiju2krona/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kaiju/kaiju2table/environment.yml b/modules/nf-core/kaiju/kaiju2table/environment.yml index 3bb316c1caf..c095312ac3f 100644 --- a/modules/nf-core/kaiju/kaiju2table/environment.yml +++ b/modules/nf-core/kaiju/kaiju2table/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kaiju/mergeoutputs/environment.yml b/modules/nf-core/kaiju/mergeoutputs/environment.yml index 3ecb973eeec..c095312ac3f 100644 --- a/modules/nf-core/kaiju/mergeoutputs/environment.yml +++ b/modules/nf-core/kaiju/mergeoutputs/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::kaiju=1.10.0" + - bioconda::kaiju=1.10.0 diff --git a/modules/nf-core/kaiju/mkfmi/environment.yml b/modules/nf-core/kaiju/mkfmi/environment.yml index 3bb316c1caf..c095312ac3f 100644 --- a/modules/nf-core/kaiju/mkfmi/environment.yml +++ b/modules/nf-core/kaiju/mkfmi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kalign/align/environment.yml b/modules/nf-core/kalign/align/environment.yml index 1e47a646888..7c30448875e 100644 --- a/modules/nf-core/kalign/align/environment.yml +++ b/modules/nf-core/kalign/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 773f42484ef..773c200c445 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 773f42484ef..773c200c445 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml index 5aa2fdb9548..84d7d76e4d1 100644 --- a/modules/nf-core/kallistobustools/count/environment.yml +++ b/modules/nf-core/kallistobustools/count/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml index 698eff03032..f8ada68f06c 100644 --- a/modules/nf-core/kallistobustools/ref/environment.yml +++ b/modules/nf-core/kallistobustools/ref/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kat/hist/environment.yml b/modules/nf-core/kat/hist/environment.yml index bde5501d43b..90b7479b11b 100644 --- a/modules/nf-core/kat/hist/environment.yml +++ b/modules/nf-core/kat/hist/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/khmer/normalizebymedian/environment.yml b/modules/nf-core/khmer/normalizebymedian/environment.yml index 66a065a0a01..0b1809c4220 100644 --- a/modules/nf-core/khmer/normalizebymedian/environment.yml +++ b/modules/nf-core/khmer/normalizebymedian/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/khmer/uniquekmers/environment.yml b/modules/nf-core/khmer/uniquekmers/environment.yml index 66a065a0a01..0b1809c4220 100644 --- a/modules/nf-core/khmer/uniquekmers/environment.yml +++ b/modules/nf-core/khmer/uniquekmers/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kleborate/environment.yml b/modules/nf-core/kleborate/environment.yml index 2c6f7bc1dfb..2e9273a679e 100644 --- a/modules/nf-core/kleborate/environment.yml +++ b/modules/nf-core/kleborate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kma/index/environment.yml b/modules/nf-core/kma/index/environment.yml index c8578084115..f4df2e0049f 100644 --- a/modules/nf-core/kma/index/environment.yml +++ b/modules/nf-core/kma/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - conda-forge dependencies: - - bioconda::kma=1.4.15 \ No newline at end of file + - bioconda::kma=1.4.15 diff --git a/modules/nf-core/kma/index/meta.yml b/modules/nf-core/kma/index/meta.yml index 32f054a962e..fe4321acb25 100644 --- a/modules/nf-core/kma/index/meta.yml +++ b/modules/nf-core/kma/index/meta.yml @@ -15,8 +15,7 @@ tools: documentation: "https://bitbucket.org/genomicepidemiology/kma/src/master/" tool_dev_url: "https://bitbucket.org/genomicepidemiology/kma/src/master/" doi: "10.1186/s12859-018-2336-6" - licence: - ["http://www.apache.org/licenses/LICENSE-2.0"] + licence: ["http://www.apache.org/licenses/LICENSE-2.0"] input: - - meta: @@ -31,20 +30,20 @@ input: output: - index: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - - 'kmaindex': - type: directory - description: Directory of KMA index files - pattern: "*.{comp.b,length.b,name,seq.b}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - "kmaindex": + type: directory + description: Directory of KMA index files + pattern: "*.{comp.b,length.b,name,seq.b}" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@krannich479" diff --git a/modules/nf-core/kmcp/compute/environment.yml b/modules/nf-core/kmcp/compute/environment.yml index ae5b92028ac..08c79f0c606 100644 --- a/modules/nf-core/kmcp/compute/environment.yml +++ b/modules/nf-core/kmcp/compute/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kmcp/index/environment.yml b/modules/nf-core/kmcp/index/environment.yml index ae5b92028ac..08c79f0c606 100644 --- a/modules/nf-core/kmcp/index/environment.yml +++ b/modules/nf-core/kmcp/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kmcp/merge/environment.yml b/modules/nf-core/kmcp/merge/environment.yml index 99b1b7bbfbf..0550ff60091 100644 --- a/modules/nf-core/kmcp/merge/environment.yml +++ b/modules/nf-core/kmcp/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kmcp/profile/environment.yml b/modules/nf-core/kmcp/profile/environment.yml index ae5b92028ac..08c79f0c606 100644 --- a/modules/nf-core/kmcp/profile/environment.yml +++ b/modules/nf-core/kmcp/profile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kmcp/search/environment.yml b/modules/nf-core/kmcp/search/environment.yml index ae5b92028ac..08c79f0c606 100644 --- a/modules/nf-core/kmcp/search/environment.yml +++ b/modules/nf-core/kmcp/search/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kofamscan/environment.yml b/modules/nf-core/kofamscan/environment.yml index a9d8ce4a54b..349fc8ef5de 100644 --- a/modules/nf-core/kofamscan/environment.yml +++ b/modules/nf-core/kofamscan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/kraken2/add/environment.yml b/modules/nf-core/kraken2/add/environment.yml index 9e63d98cc04..54b83e4892c 100644 --- a/modules/nf-core/kraken2/add/environment.yml +++ b/modules/nf-core/kraken2/add/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::kraken2=2.1.3" - - "coreutils=9.4" - - "pigz=2.8" + - bioconda::kraken2=2.1.3 + - coreutils=9.4 + - pigz=2.8 diff --git a/modules/nf-core/kraken2/build/environment.yml b/modules/nf-core/kraken2/build/environment.yml index 9e63d98cc04..54b83e4892c 100644 --- a/modules/nf-core/kraken2/build/environment.yml +++ b/modules/nf-core/kraken2/build/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::kraken2=2.1.3" - - "coreutils=9.4" - - "pigz=2.8" + - bioconda::kraken2=2.1.3 + - coreutils=9.4 + - pigz=2.8 diff --git a/modules/nf-core/kraken2/buildstandard/environment.yml b/modules/nf-core/kraken2/buildstandard/environment.yml index 9e63d98cc04..54b83e4892c 100644 --- a/modules/nf-core/kraken2/buildstandard/environment.yml +++ b/modules/nf-core/kraken2/buildstandard/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::kraken2=2.1.3" - - "coreutils=9.4" - - "pigz=2.8" + - bioconda::kraken2=2.1.3 + - coreutils=9.4 + - pigz=2.8 diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml index ba776d315eb..54b83e4892c 100644 --- a/modules/nf-core/kraken2/kraken2/environment.yml +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -1,7 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::kraken2=2.1.3" - - "coreutils=9.4" - - "pigz=2.8" + - bioconda::kraken2=2.1.3 + - coreutils=9.4 + - pigz=2.8 diff --git a/modules/nf-core/krakentools/combinekreports/environment.yml b/modules/nf-core/krakentools/combinekreports/environment.yml index 13814bc27e1..8f5eacfd37c 100644 --- a/modules/nf-core/krakentools/combinekreports/environment.yml +++ b/modules/nf-core/krakentools/combinekreports/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krakentools/extractkrakenreads/environment.yml b/modules/nf-core/krakentools/extractkrakenreads/environment.yml index c35d4f25bec..8f5eacfd37c 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/environment.yml +++ b/modules/nf-core/krakentools/extractkrakenreads/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::krakentools=1.2" + - bioconda::krakentools=1.2 diff --git a/modules/nf-core/krakentools/kreport2krona/environment.yml b/modules/nf-core/krakentools/kreport2krona/environment.yml index 13814bc27e1..8f5eacfd37c 100644 --- a/modules/nf-core/krakentools/kreport2krona/environment.yml +++ b/modules/nf-core/krakentools/kreport2krona/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krakenuniq/build/environment.yml b/modules/nf-core/krakenuniq/build/environment.yml index bbf85c33574..225214d3843 100644 --- a/modules/nf-core/krakenuniq/build/environment.yml +++ b/modules/nf-core/krakenuniq/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krakenuniq/download/environment.yml b/modules/nf-core/krakenuniq/download/environment.yml index bbf85c33574..225214d3843 100644 --- a/modules/nf-core/krakenuniq/download/environment.yml +++ b/modules/nf-core/krakenuniq/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml index bbf85c33574..225214d3843 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krona/kronadb/environment.yml b/modules/nf-core/krona/kronadb/environment.yml index cb06934b14e..d28b095df5e 100644 --- a/modules/nf-core/krona/kronadb/environment.yml +++ b/modules/nf-core/krona/kronadb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krona/ktimporttaxonomy/environment.yml b/modules/nf-core/krona/ktimporttaxonomy/environment.yml index 342c589237f..9c782b4a936 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/environment.yml +++ b/modules/nf-core/krona/ktimporttaxonomy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krona/ktimporttext/environment.yml b/modules/nf-core/krona/ktimporttext/environment.yml index 342c589237f..9c782b4a936 100644 --- a/modules/nf-core/krona/ktimporttext/environment.yml +++ b/modules/nf-core/krona/ktimporttext/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml index cb06934b14e..d28b095df5e 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml +++ b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml index 7db722d9b7c..dfa402574aa 100644 --- a/modules/nf-core/last/dotplot/environment.yml +++ b/modules/nf-core/last/dotplot/environment.yml @@ -1,6 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::last=1608 + - conda-forge::open-fonts=0.7.0 diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index 963965bd1c3..5a35cf8f22c 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -4,13 +4,14 @@ process LAST_DOTPLOT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' - : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a35d17772276115874eda45f17b05407c9855ecec8c11d39cce49f0028f44cfb/data' + : 'community.wave.seqera.io/library/last_open-fonts:f1048938520a62ad'}" input: tuple val(meta), path(maf), path(annot_b) tuple val(meta2), path(annot_a) val(format) + val(filter) output: tuple val(meta), path("*.gif"), optional:true, emit: gif @@ -22,15 +23,21 @@ process LAST_DOTPLOT { script: def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def annot_a_arg = annot_a ? "-a ${annot_a}" : '' def annot_b_arg = annot_b ? "-b ${annot_b}" : '' + def input_command = filter ? "maf-linked ${args2}" : "zcat -f" """ + TTF=/home/ubuntu/conda_pkgs_dir/open-fonts-0.7.0-1/fonts/open-fonts/DejaVuSansMono-Regular.ttf + [ -e "\$TTF" ] || TTF="/opt/conda/fonts/open-fonts/DejaVuSansMono-Regular.ttf" + $input_command $maf | last-dotplot \\ + -f \$TTF \\ $args \\ $annot_a_arg \\ $annot_b_arg \\ - $maf \\ + - \\ $prefix.$format # last-dotplot has no --version option so let's use lastal from the same suite diff --git a/modules/nf-core/last/dotplot/meta.yml b/modules/nf-core/last/dotplot/meta.yml index 58579b96a40..8599d0767ea 100644 --- a/modules/nf-core/last/dotplot/meta.yml +++ b/modules/nf-core/last/dotplot/meta.yml @@ -43,6 +43,9 @@ input: - - format: type: string description: Output format (PNG or GIF). + - - filter: + type: boolean + description: Remove isolated alignments using the `maf-linked` software. output: - gif: - meta: diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test b/modules/nf-core/last/dotplot/tests/main.nf.test index 3ea403820d2..56805ea354c 100644 --- a/modules/nf-core/last/dotplot/tests/main.nf.test +++ b/modules/nf-core/last/dotplot/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { . collectFile(name: 'dummy_annot_a.bed', newLine: true) . map { [ [ id:'test'], it ] } input[2] = channel.of("png") + input[3] = channel.of([]) """ } } @@ -32,8 +33,37 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert process.out.png.get(0).get(1).endsWith("test.png") } + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - contigs - genome - png - filter") { + + when { + process { + """ + input[0] = channel.of('NODE_1_length_20973_cov_191.628754\t2000\t2010') + . collectFile(name: 'dummy_annot_b.bed', newLine: true) + . map { [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true), + it + ] } + input[1] = channel.of('MT192765.1\t1000\t1010') + . collectFile(name: 'dummy_annot_a.bed', newLine: true) + . map { [ [ id:'test'], it ] } + input[2] = channel.of("png") + input[3] = channel.of("filter") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ) } @@ -51,6 +81,7 @@ nextflow_process { ] input[1] = [ [id: 'test'], [] ] input[2] = "gif" + input[3] = [] """ } } @@ -58,8 +89,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert process.out.gif.get(0).get(1).endsWith("test.gif") } + { assert snapshot(process.out).match() } ) } @@ -78,6 +108,7 @@ nextflow_process { ] input[1] = [ [id: 'test'], [] ] input[2] = "png" + input[3] = [] """ } } @@ -85,8 +116,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert process.out.png.get(0).get(1).endsWith("test.png") } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap index 3676f0f4c20..ab8078fda5e 100644 --- a/modules/nf-core/last/dotplot/tests/main.nf.test.snap +++ b/modules/nf-core/last/dotplot/tests/main.nf.test.snap @@ -1,38 +1,158 @@ { "sarscov2 - contigs - genome - gif": { "content": [ - [ - "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.gif:md5,cec730f1d060a82553cefe2311708bad" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ], + "gif": [ + [ + { + "id": "test" + }, + "test.gif:md5,cec730f1d060a82553cefe2311708bad" + ] + ], + "png": [ + + ], + "versions": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T09:18:32.629314" + "timestamp": "2025-02-03T09:27:56.241408" }, "sarscov2 - contigs - genome - png - stub": { "content": [ - [ - "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ], + "gif": [ + + ], + "png": [ + [ + { + "id": "test" + }, + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T09:18:48.084683" + "timestamp": "2025-01-31T09:55:40.665796" + }, + "sarscov2 - contigs - genome - png - filter": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.png:md5,9e3892ca780f112fc0266543455ce9e5" + ] + ], + "2": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ], + "gif": [ + + ], + "png": [ + [ + { + "id": "test" + }, + "test.png:md5,9e3892ca780f112fc0266543455ce9e5" + ] + ], + "versions": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-04T16:58:29.410356" }, "sarscov2 - contigs - genome - png": { "content": [ - [ - "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.png:md5,005267881455bdab7c8bd87ec27060f8" + ] + ], + "2": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ], + "gif": [ + + ], + "png": [ + [ + { + "id": "test" + }, + "test.png:md5,005267881455bdab7c8bd87ec27060f8" + ] + ], + "versions": [ + "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7" + ] + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T09:18:17.971205" + "timestamp": "2025-02-03T09:27:41.83809" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/lastal/environment.yml +++ b/modules/nf-core/last/lastal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/lastdb/environment.yml +++ b/modules/nf-core/last/lastdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml index 7db722d9b7c..71872006467 100644 --- a/modules/nf-core/last/mafconvert/environment.yml +++ b/modules/nf-core/last/mafconvert/environment.yml @@ -1,6 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::last=1608 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 3f02ed7bfeb..648dd710877 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -4,24 +4,29 @@ process LAST_MAFCONVERT { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data' - : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/379183a78f725c3a8f2c4dda2f73ad452e57cc895239938fc97281d7bd74ffbf/data' + : 'community.wave.seqera.io/library/last_samtools:e2b51d2d9a1ce9fa'}" input: tuple val(meta), path(maf) val(format) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) output: - tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz - tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz - tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz - tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz - tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz - tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz - tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz - tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz - tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz - path "versions.yml" , emit: versions + tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz + tuple val(meta), path("*.bam"), optional:true, emit: bam + tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz + tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz + tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz + tuple val(meta), path("*.cram"), path(fasta), optional:true, emit: cram + tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz + tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz + tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz + tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz + tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -31,7 +36,19 @@ process LAST_MAFCONVERT { def prefix = task.ext.prefix ?: "${meta.id}" """ set -o pipefail - maf-convert $args $format $maf | gzip --no-name > ${prefix}.${format}.gz + + case $format in + bam) + maf-convert $args -d sam $maf | samtools view -b -o ${prefix}.${format} + ;; + cram) + # CRAM output is not supported if the genome is compressed with something else than bgzip + maf-convert $args -d sam $maf | samtools view -Ct $fasta -o ${prefix}.${format} + ;; + *) + maf-convert $args $format $maf | gzip --no-name > ${prefix}.${format}.gz + ;; + esac # maf-convert has no --version option but lastdb (part of the same package) has. cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/last/mafconvert/meta.yml b/modules/nf-core/last/mafconvert/meta.yml index 4b9d2cff8a1..ac177a8d78f 100644 --- a/modules/nf-core/last/mafconvert/meta.yml +++ b/modules/nf-core/last/mafconvert/meta.yml @@ -29,6 +29,35 @@ input: type: string description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab) + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Genome file in FASTA format for CRAM conversion. If compressed it + must be done in BGZF format (like with the bgzip tool). + pattern: "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fai: + type: file + description: Genome index file needed for CRAM conversion. + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gzi: + type: file + description: Genome index file needed for CRAM conversion when the genome file + was compressed with the BGZF algorithm. + pattern: "*.gzi" output: - axt_gz: - meta: @@ -40,6 +69,16 @@ output: type: file description: Gzipped pairwise alignment in Axt (Blastz) format (optional) pattern: "*.axt.gz" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Pairwise alignment in BAM format (optional) + pattern: "*.bam" - blast_gz: - meta: type: map @@ -70,6 +109,20 @@ output: type: file description: Gzipped pairwise alignment in UCSC chain format (optional) pattern: "*.chain.gz" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.cram": + type: file + description: Pairwise alignment in CRAM format (optional) + pattern: "*.cram" + - fasta: + type: file + description: Genome file to recover sequences from the CRAM file (optional) + pattern: "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}" - gff_gz: - meta: type: map diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test b/modules/nf-core/last/mafconvert/tests/main.nf.test index ea21d1f62b6..343c183e462 100644 --- a/modules/nf-core/last/mafconvert/tests/main.nf.test +++ b/modules/nf-core/last/mafconvert/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "last" tag "last/mafconvert" - test("sarscov2 - bam") { + test("sarscov2 - psl") { when { process { @@ -19,6 +19,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] input[1] = 'psl' + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] """ } } @@ -32,7 +35,71 @@ nextflow_process { } - test("sarscov2 - bam - stub") { + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = [ + [ id:'contigs.genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + input[1] = 'bam' + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getSamLines() }, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - cram") { + + when { + process { + """ + input[0] = [ + [ id:'contigs.genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + input[1] = 'cram' + input[2] = [ + [ id:'contigs.genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ + [ id:'contigs.genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[4] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.cram.collect { cram(it[1], it[2]).getSamLines() }, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - psl - stub") { options "-stub" when { @@ -43,6 +110,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] input[1] = 'psl' + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] """ } } diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap index 8525a41cc4a..dfb755c5064 100644 --- a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap +++ b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "sarscov2 - bam - stub": { + "sarscov2 - psl": { "content": [ { "0": [ @@ -7,6 +7,12 @@ ], "1": [ + ], + "10": [ + + ], + "11": [ + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" ], "2": [ @@ -21,23 +27,26 @@ ], "6": [ + + ], + "7": [ + + ], + "8": [ [ { "id": "contigs.genome" }, - "contigs.genome.psl.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + "contigs.genome.psl.gz:md5,515d3cff55d159309bedd38f47dd034b" ] ], - "7": [ + "9": [ ], - "8": [ + "axt_gz": [ ], - "9": [ - "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" - ], - "axt_gz": [ + "bam": [ ], "blast_gz": [ @@ -48,6 +57,9 @@ ], "chain_gz": [ + ], + "cram": [ + ], "gff_gz": [ @@ -60,7 +72,7 @@ { "id": "contigs.genome" }, - "contigs.genome.psl.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + "contigs.genome.psl.gz:md5,515d3cff55d159309bedd38f47dd034b" ] ], "sam_gz": [ @@ -76,11 +88,33 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-22T10:17:48.535961" + "timestamp": "2025-01-30T10:31:47.133387" }, - "sarscov2 - bam": { + "sarscov2 - cram": { + "content": [ + [ + [ + "NODE_1_length_20973_cov_191.628754\t16\tMT192765.1\t8882\t255\t20948M25H\t*\t0\t0\tGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAAGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACTTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTGGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCC\t*\tAS:i:128566\tEV:Z:0\n", + 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"chain_gz": [ + ], + "cram": [ + ], "gff_gz": [ @@ -141,7 +187,7 @@ { "id": "contigs.genome" }, - "contigs.genome.psl.gz:md5,515d3cff55d159309bedd38f47dd034b" + "contigs.genome.psl.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "sam_gz": [ @@ -157,8 +203,30 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-30T10:32:31.669726" + }, + "sarscov2 - bam": { + "content": [ + [ + [ + "NODE_1_length_20973_cov_191.628754\t16\tMT192765.1\t8882\t255\t2830=1X7094=1X1453=1X9568=25H\t*\t0\t0\tGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAAGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACTTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTGGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCC\t*\tNM:i:3\tAS:i:128566\tEV:Z:0\n", + "NODE_2_length_8774_cov_178.827802\t0\tMT192765.1\t25\t255\t5H8649=120H\t*\t0\t0\tCCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTTTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAACTCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCAGATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCAGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTATGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTTTCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAAATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAGTTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAACCATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAACCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGTGATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAACCTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTGTCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGAAAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTGCTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTATTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAGCAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAATTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTACTCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAGGCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCTTAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAATGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCTATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTCTTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATCTTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTTGTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAGGTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGTGATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAATGTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACTAGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTTACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTGGTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGATATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAGAATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAGCACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTTTGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA\t*\tNM:i:0\tAS:i:53031\tEV:Z:0\n", + "NODE_2_length_8774_cov_178.827802\t0\tMT192765.1\t12929\t255\t8647H127=\t*\t0\t0\tAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGT\t*\tNM:i:0\tAS:i:776\tEV:Z:5.2e-67\n", + "NODE_2_length_8774_cov_178.827802\t16\tMT192765.1\t5738\t255\t3036H20=5718H\t*\t0\t0\tACACTGGTAATTACCAGTGT\t*\tNM:i:0\tAS:i:124\tEV:Z:0.00027\n", + "NODE_5_length_446_cov_1.078370\t0\tMT192765.1\t60\t255\t102H16=1X124=1X124=1X77=\t*\t0\t0\tTAAACGAACTTTAAAAACTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCATGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGATCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATG\t*\tNM:i:3\tAS:i:2104\tEV:Z:1e-196\n", + "NODE_5_length_446_cov_1.078370\t0\tMT192765.1\t25273\t255\t113=333H\t*\t0\t0\tTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTT\t*\tNM:i:0\tAS:i:709\tEV:Z:5.4e-62\n" + ] + ], + [ + "versions.yml:md5,7c66667735aa9f79367b8b8fc8df4497" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2025-01-22T10:17:13.689118" + "timestamp": "2025-01-31T21:57:36.433274" } } \ No newline at end of file diff --git a/modules/nf-core/last/mafswap/environment.yml b/modules/nf-core/last/mafswap/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/mafswap/environment.yml +++ b/modules/nf-core/last/mafswap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/postmask/environment.yml b/modules/nf-core/last/postmask/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/postmask/environment.yml +++ b/modules/nf-core/last/postmask/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/split/environment.yml b/modules/nf-core/last/split/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/split/environment.yml +++ b/modules/nf-core/last/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/train/environment.yml b/modules/nf-core/last/train/environment.yml index 7db722d9b7c..8b71dfd2836 100644 --- a/modules/nf-core/last/train/environment.yml +++ b/modules/nf-core/last/train/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/learnmsa/align/environment.yml b/modules/nf-core/learnmsa/align/environment.yml index 1c1d69fd765..0c4cd942239 100644 --- a/modules/nf-core/learnmsa/align/environment.yml +++ b/modules/nf-core/learnmsa/align/environment.yml @@ -1,6 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::learnmsa=2.0.1 - - conda-forge::pigz=2.8 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/learnmsa/align/main.nf b/modules/nf-core/learnmsa/align/main.nf index 304fb07ced6..c9d40fd7221 100644 --- a/modules/nf-core/learnmsa/align/main.nf +++ b/modules/nf-core/learnmsa/align/main.nf @@ -1,37 +1,33 @@ process LEARNMSA_ALIGN { tag "$meta.id" label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-741e0da5cf2d6d964f559672e2908c2111cbb46b:4930edd009376542543bfd2e20008bb1ae58f841-0' : - 'biocontainers/mulled-v2-741e0da5cf2d6d964f559672e2908c2111cbb46b:4930edd009376542543bfd2e20008bb1ae58f841-0' }" + container "registry.hub.docker.com/felbecker/learnmsa:2.0.9" input: tuple val(meta), path(fasta) - val(compress) output: - tuple val(meta), path("*.aln{.gz,}"), emit: alignment + tuple val(meta), path("*.aln") , emit: alignment path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def write_output = compress ? ">(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "${prefix}.aln" + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error("LearnMSA align module does not support Conda. Please use Docker / Singularity / Podman instead.") + } """ learnMSA \\ - $args \\ - -i <(unpigz -cdf $fasta) \\ - -o $write_output + -i $fasta \\ + -o "${prefix}.aln" \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": learnmsa: \$(learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g') - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) END_VERSIONS """ @@ -39,12 +35,11 @@ process LEARNMSA_ALIGN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.aln${compress ? '.gz' : ''} + touch ${prefix}.aln cat <<-END_VERSIONS > versions.yml "${task.process}": - learnmsa: \$(learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g') - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) + learnmsa: \$(if command -v learnMSA &>/dev/null; then learnMSA -h | grep 'version' | awk -F 'version ' '{print \$2}' | awk '{print \$1}' | sed 's/)//g'; else echo "STUB_TEST_HARDCODED_VERSION"; fi) END_VERSIONS """ } diff --git a/modules/nf-core/learnmsa/align/meta.yml b/modules/nf-core/learnmsa/align/meta.yml index b3e549fea7b..7cd4a63c4ee 100644 --- a/modules/nf-core/learnmsa/align/meta.yml +++ b/modules/nf-core/learnmsa/align/meta.yml @@ -21,13 +21,8 @@ input: e.g. `[ id:'test']` - fasta: type: file - description: Input sequences in FASTA format. May be gz-compressed or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. - Set to true to enable/false to disable compression. Compression is done using - pigz, and is multithreaded. + description: Input sequences in FASTA format. + pattern: "*.{fa,fasta}" output: - alignment: - meta: @@ -35,10 +30,10 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'test']` - - "*.aln{.gz,}": + - "*.aln": type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed. - pattern: "*.aln{.gz,}" + description: Alignment file, in FASTA format. + pattern: "*.aln" - versions: - versions.yml: type: file diff --git a/modules/nf-core/learnmsa/align/tests/main.nf.test b/modules/nf-core/learnmsa/align/tests/main.nf.test index 8459ead38d5..9432414fbaa 100644 --- a/modules/nf-core/learnmsa/align/tests/main.nf.test +++ b/modules/nf-core/learnmsa/align/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process LEARNMSA_ALIGN" + config "./nextflow.config" script "../main.nf" process "LEARNMSA_ALIGN" @@ -10,15 +11,15 @@ nextflow_process { tag "learnmsa" tag "learnmsa/align" - test("sarscov2 - fasta - uncompressed") { + test("seatoxin - stub") { + options "-stub" when { process { """ - input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] - input[1] = false """ } } @@ -26,31 +27,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.alignment.get(0).get(1)).getText().contains(">sample1") }, - { assert snapshot(process.out.versions).match("versions") } - ) - } - - } - - test("sarscov2 - fasta - compressed") { - - when { - process { - """ - input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) - ] - input[1] = true - """ - } - } + { assert snapshot ( process.out ).match() } - then { - assertAll( - { assert process.success }, - { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains(">sample1") }, - { assert snapshot(process.out.versions).match("versions1") } ) } diff --git a/modules/nf-core/learnmsa/align/tests/main.nf.test.snap b/modules/nf-core/learnmsa/align/tests/main.nf.test.snap index 981738a276d..5c54c14416e 100644 --- a/modules/nf-core/learnmsa/align/tests/main.nf.test.snap +++ b/modules/nf-core/learnmsa/align/tests/main.nf.test.snap @@ -1,26 +1,35 @@ { - "versions": { + "seatoxin - stub": { "content": [ - [ - "versions.yml:md5,85322b0f038aa768f202fd0d748d6c7c" - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,c3886d32309d141ad22aba3a8a119d62" + ], + "alignment": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c3886d32309d141ad22aba3a8a119d62" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-03-20T16:06:48.867020809" - }, - "versions1": { - "content": [ - [ - "versions.yml:md5,85322b0f038aa768f202fd0d748d6c7c" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-20T16:12:13.921813607" + "timestamp": "2025-01-31T13:29:53.669503397" } } \ No newline at end of file diff --git a/modules/nf-core/learnmsa/align/tests/nextflow.config b/modules/nf-core/learnmsa/align/tests/nextflow.config new file mode 100644 index 00000000000..2c4d3e22697 --- /dev/null +++ b/modules/nf-core/learnmsa/align/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + + // The container is overwritten because the original container is 13GB + // and it cannot be currently run on the runners. + // Tests are run in stub using this container instead. + withName: LEARNMSA_ALIGN{ + container = "nf-core/ubuntu:22.04" + } + +} diff --git a/modules/nf-core/leehom/environment.yml b/modules/nf-core/leehom/environment.yml index eaae12b1a54..cc93ca38bed 100644 --- a/modules/nf-core/leehom/environment.yml +++ b/modules/nf-core/leehom/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/legsta/environment.yml b/modules/nf-core/legsta/environment.yml index ca9f7ef3e7b..e721dcfafb7 100644 --- a/modules/nf-core/legsta/environment.yml +++ b/modules/nf-core/legsta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/leviosam2/index/environment.yml b/modules/nf-core/leviosam2/index/environment.yml index 2998a4af4e4..4200a350638 100644 --- a/modules/nf-core/leviosam2/index/environment.yml +++ b/modules/nf-core/leviosam2/index/environment.yml @@ -1,6 +1,7 @@ --- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::leviosam2=0.4.2" + - bioconda::leviosam2=0.4.2 diff --git a/modules/nf-core/leviosam2/lift/environment.yml b/modules/nf-core/leviosam2/lift/environment.yml index 2998a4af4e4..4200a350638 100644 --- a/modules/nf-core/leviosam2/lift/environment.yml +++ b/modules/nf-core/leviosam2/lift/environment.yml @@ -1,6 +1,7 @@ --- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::leviosam2=0.4.2" + - bioconda::leviosam2=0.4.2 diff --git a/modules/nf-core/liftoff/environment.yml b/modules/nf-core/liftoff/environment.yml index 94c10a3dfce..bdac6d51cf4 100644 --- a/modules/nf-core/liftoff/environment.yml +++ b/modules/nf-core/liftoff/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/liftoff/main.nf b/modules/nf-core/liftoff/main.nf index 4db5da2f462..8bf48d3cfa9 100644 --- a/modules/nf-core/liftoff/main.nf +++ b/modules/nf-core/liftoff/main.nf @@ -9,7 +9,7 @@ process LIFTOFF { input: tuple val(meta), path(target_fa) - path ref_fa, name: 'ref_assembly.fa' + path ref_fa, name: 'ref/*' path ref_annotation path ref_db @@ -28,6 +28,22 @@ process LIFTOFF { def arg_db = ref_db ? "-db $ref_db" : '' prefix = task.ext.prefix ?: "${meta.id}" """ + if [[ ${target_fa} == *.gz ]]; then + zcat ${target_fa} > target.fasta + fi + + if [[ ${target_fa} != *.gz ]]; then + ln -s ${target_fa} target.fasta + fi + + if [[ ${ref_fa} == *.gz ]]; then + zcat ${ref_fa} > reference.fasta + fi + + if [[ ${ref_fa} != *.gz ]]; then + ln -s ${ref_fa} reference.fasta + fi + liftoff \\ $arg_g \\ $arg_db \\ @@ -35,8 +51,8 @@ process LIFTOFF { -o "${prefix}.gff3" \\ -u "${prefix}.unmapped.txt" \\ $args \\ - $target_fa \\ - ref_assembly.fa + target.fasta \\ + reference.fasta mv \\ "${prefix}.gff3_polished" \\ diff --git a/modules/nf-core/liftoff/meta.yml b/modules/nf-core/liftoff/meta.yml index a8ed079fbd5..7d809f7f4f5 100644 --- a/modules/nf-core/liftoff/meta.yml +++ b/modules/nf-core/liftoff/meta.yml @@ -28,12 +28,12 @@ input: e.g. `[ id:'test' ]` - target_fa: type: file - description: Target assembly in fasta format - pattern: "*.{fsa,fa,fasta}" + description: Target assembly in fasta format (can be gzipped) + pattern: "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}" - - ref_fa: type: file - description: Reference assembly in fasta format - pattern: "*.{fsa,fa,fasta}" + description: Reference assembly in fasta format (can be gzipped) + pattern: "*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}" - - ref_annotation: type: file description: Reference assembly annotations in gtf or gff3 format diff --git a/modules/nf-core/liftoff/tests/main.nf.test b/modules/nf-core/liftoff/tests/main.nf.test index c8ebf261ec3..2a17cc81775 100644 --- a/modules/nf-core/liftoff/tests/main.nf.test +++ b/modules/nf-core/liftoff/tests/main.nf.test @@ -7,26 +7,10 @@ nextflow_process { tag "modules" tag "modules_nfcore" - tag "nf-core/gunzip" tag "liftoff" - tag "gunzip" test("homo_sapiens-genome_21_fasta-genome_1_fasta-genome_1_gtf") { - setup { - run("GUNZIP") { - script "../../../nf-core/gunzip" - - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.fasta.gz', checkIfExists: true) - ] - """ - } - } - } when { process { @@ -35,7 +19,9 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] - input[1] = GUNZIP.out.gunzip.map { meta, file -> file } + input[1] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.gtf', checkIfExists: true) ] @@ -59,21 +45,6 @@ nextflow_process { test("homo_sapiens-genome_21_fasta-genome_1_fasta-genome_1_gtf-stub") { options '-stub' - setup { - run("GUNZIP") { - script "../../../nf-core/gunzip" - - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.fasta.gz', checkIfExists: true) - ] - """ - } - } - } - when { process { """ @@ -81,7 +52,9 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ] - input[1] = GUNZIP.out.gunzip.map { meta, file -> file } + input[1] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr1/genome.gtf', checkIfExists: true) ] diff --git a/modules/nf-core/lima/environment.yml b/modules/nf-core/lima/environment.yml index 7c13724537a..2e56e30d8bf 100644 --- a/modules/nf-core/lima/environment.yml +++ b/modules/nf-core/lima/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/limma/differential/environment.yml b/modules/nf-core/limma/differential/environment.yml index 5ff03f6cef3..d0a5d902d59 100644 --- a/modules/nf-core/limma/differential/environment.yml +++ b/modules/nf-core/limma/differential/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lissero/environment.yml b/modules/nf-core/lissero/environment.yml index 81e172e4051..7b5ea4de71b 100644 --- a/modules/nf-core/lissero/environment.yml +++ b/modules/nf-core/lissero/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/alnqual/environment.yml b/modules/nf-core/lofreq/alnqual/environment.yml index 15312b90a64..ecb64f9dbec 100644 --- a/modules/nf-core/lofreq/alnqual/environment.yml +++ b/modules/nf-core/lofreq/alnqual/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/call/environment.yml b/modules/nf-core/lofreq/call/environment.yml index 011ce6cbda3..4ade529a78a 100644 --- a/modules/nf-core/lofreq/call/environment.yml +++ b/modules/nf-core/lofreq/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/callparallel/environment.yml b/modules/nf-core/lofreq/callparallel/environment.yml index 011ce6cbda3..4ade529a78a 100644 --- a/modules/nf-core/lofreq/callparallel/environment.yml +++ b/modules/nf-core/lofreq/callparallel/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/filter/environment.yml b/modules/nf-core/lofreq/filter/environment.yml index 011ce6cbda3..4ade529a78a 100644 --- a/modules/nf-core/lofreq/filter/environment.yml +++ b/modules/nf-core/lofreq/filter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/indelqual/environment.yml b/modules/nf-core/lofreq/indelqual/environment.yml index 011ce6cbda3..4ade529a78a 100644 --- a/modules/nf-core/lofreq/indelqual/environment.yml +++ b/modules/nf-core/lofreq/indelqual/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/somatic/environment.yml b/modules/nf-core/lofreq/somatic/environment.yml index 011ce6cbda3..4ade529a78a 100644 --- a/modules/nf-core/lofreq/somatic/environment.yml +++ b/modules/nf-core/lofreq/somatic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/lofreq/viterbi/environment.yml b/modules/nf-core/lofreq/viterbi/environment.yml index 15312b90a64..ecb64f9dbec 100644 --- a/modules/nf-core/lofreq/viterbi/environment.yml +++ b/modules/nf-core/lofreq/viterbi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/longphase/haplotag/environment.yml b/modules/nf-core/longphase/haplotag/environment.yml index 06445a930d7..65c58ba3d35 100644 --- a/modules/nf-core/longphase/haplotag/environment.yml +++ b/modules/nf-core/longphase/haplotag/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::longphase=1.7.3" + - bioconda::longphase=1.7.3 diff --git a/modules/nf-core/longphase/phase/environment.yml b/modules/nf-core/longphase/phase/environment.yml index bb2d0eeebd1..068a22cde9c 100644 --- a/modules/nf-core/longphase/phase/environment.yml +++ b/modules/nf-core/longphase/phase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ltrfinder/environment.yml b/modules/nf-core/ltrfinder/environment.yml index 2932d5cfc9d..05cfe3aa9f8 100644 --- a/modules/nf-core/ltrfinder/environment.yml +++ b/modules/nf-core/ltrfinder/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ltr_finder_parallel=1.1" + - bioconda::ltr_finder_parallel=1.1 diff --git a/modules/nf-core/ltrharvest/environment.yml b/modules/nf-core/ltrharvest/environment.yml index c6cac36f599..ef306402845 100644 --- a/modules/nf-core/ltrharvest/environment.yml +++ b/modules/nf-core/ltrharvest/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ltr_harvest_parallel=1.1" + - bioconda::ltr_harvest_parallel=1.1 diff --git a/modules/nf-core/ltrretriever/lai/environment.yml b/modules/nf-core/ltrretriever/lai/environment.yml index f1c392a2c00..fdc63a5731d 100644 --- a/modules/nf-core/ltrretriever/lai/environment.yml +++ b/modules/nf-core/ltrretriever/lai/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::LTR_retriever=2.9.9" + - bioconda::LTR_retriever=2.9.9 diff --git a/modules/nf-core/ltrretriever/ltrretriever/environment.yml b/modules/nf-core/ltrretriever/ltrretriever/environment.yml index f1c392a2c00..fdc63a5731d 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/environment.yml +++ b/modules/nf-core/ltrretriever/ltrretriever/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::LTR_retriever=2.9.9" + - bioconda::LTR_retriever=2.9.9 diff --git a/modules/nf-core/macrel/contigs/environment.yml b/modules/nf-core/macrel/contigs/environment.yml index bb5ce1a6e68..ea2b6ac69ba 100644 --- a/modules/nf-core/macrel/contigs/environment.yml +++ b/modules/nf-core/macrel/contigs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/macs2/callpeak/environment.yml b/modules/nf-core/macs2/callpeak/environment.yml index caa3ed9f096..0e025e9d14e 100644 --- a/modules/nf-core/macs2/callpeak/environment.yml +++ b/modules/nf-core/macs2/callpeak/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::macs2=2.2.9.1" + - bioconda::macs2=2.2.9.1 diff --git a/modules/nf-core/macs3/callpeak/environment.yml b/modules/nf-core/macs3/callpeak/environment.yml index 4aa6a32ddd5..a0fb8b93943 100644 --- a/modules/nf-core/macs3/callpeak/environment.yml +++ b/modules/nf-core/macs3/callpeak/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::macs3=3.0.1" + - bioconda::macs3=3.0.1 diff --git a/modules/nf-core/mafft/align/environment.yml b/modules/nf-core/mafft/align/environment.yml index 97a13e685ee..7e83ae6aadd 100644 --- a/modules/nf-core/mafft/align/environment.yml +++ b/modules/nf-core/mafft/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mafft/guidetree/environment.yml b/modules/nf-core/mafft/guidetree/environment.yml index a43c6dd1adc..ed4e60319fe 100644 --- a/modules/nf-core/mafft/guidetree/environment.yml +++ b/modules/nf-core/mafft/guidetree/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mafft=7.525" + - bioconda::mafft=7.525 diff --git a/modules/nf-core/mageck/count/environment.yml b/modules/nf-core/mageck/count/environment.yml index 7cc6f888022..2440b706eaa 100644 --- a/modules/nf-core/mageck/count/environment.yml +++ b/modules/nf-core/mageck/count/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mageck/mle/environment.yml b/modules/nf-core/mageck/mle/environment.yml index 7cc6f888022..2440b706eaa 100644 --- a/modules/nf-core/mageck/mle/environment.yml +++ b/modules/nf-core/mageck/mle/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mageck/test/environment.yml b/modules/nf-core/mageck/test/environment.yml index 7cc6f888022..2440b706eaa 100644 --- a/modules/nf-core/mageck/test/environment.yml +++ b/modules/nf-core/mageck/test/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/magus/align/environment.yml b/modules/nf-core/magus/align/environment.yml index 2934cc977cc..cc71be1cc7a 100644 --- a/modules/nf-core/magus/align/environment.yml +++ b/modules/nf-core/magus/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/magus/guidetree/environment.yml b/modules/nf-core/magus/guidetree/environment.yml index 423a598583b..9fb4aa7a683 100644 --- a/modules/nf-core/magus/guidetree/environment.yml +++ b/modules/nf-core/magus/guidetree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/malt/build/environment.yml b/modules/nf-core/malt/build/environment.yml index 2e3a66a93e3..e6d570b0347 100644 --- a/modules/nf-core/malt/build/environment.yml +++ b/modules/nf-core/malt/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index b0f22492287..5939c40bbe3 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -9,6 +9,7 @@ process MALT_BUILD { path fastas, stageAs: 'fa_folder/' path gff path mapping_db + val map_type output: path "malt_index/", emit: index @@ -21,16 +22,17 @@ process MALT_BUILD { script: def args = task.ext.args ?: '' def igff = gff ? "-igff ${gff}" : "" - """ + INDEX=`find -L . -name '*.db' -o -name '*.abin' -type f` + echo \$INDEX malt-build \\ ${args} \\ -v \\ - --input fa_folder \\ + --input fa_folder/ \\ ${igff} \\ -d 'malt_index/' \\ -t ${task.cpus} \\ - -mdb ${mapping_db}/*.db |&tee malt-build.log + -${map_type} \$INDEX |&tee malt-build.log cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml index 099030a4943..9abe5842233 100644 --- a/modules/nf-core/malt/build/meta.yml +++ b/modules/nf-core/malt/build/meta.yml @@ -31,8 +31,12 @@ input: pattern: "*/|*.gff|*.gff3" - - mapping_db: type: file - description: MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html - pattern: "*.db" + description: An uncompressed MEGAN mapping file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html (either mapping db, or acc2* .abin file) + pattern: "*.{db,abin}" + - - map_type: + type: string + description: The type of map file provided to the pipeline. Must be a valid string corresponding to a single-dash parameter, for example '-a2tax' or '-a2interpro2go' + pattern: "mdb|a2t|s2t|a2ec|s2ec|t4ec|a2eggnog|s2eggnog|t4eggnog|a2gtdb|s2gtdb|t4gtdb|a2interpro2go|s2interpro2go|t4interprotogo|a2kegg|s2kegg|t4kegg|a2pgpt|s2pgpt|t4pgpt|a2seed|s2seed|t4seed" output: - index: - malt_index/: diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index a2a0db8b242..d1e9914c018 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -10,19 +10,74 @@ nextflow_process { tag "malt/build" tag "unzip" - setup { - run("UNZIP") { - script "../../../unzip/main.nf" + test("sarscov2 - fastq - mdb") { + config "./nextflow.config" + + setup { + run("UNZIP", alias: "UNZIP_MDB") { + script "../../../unzip/main.nf" + process { + """ + input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] + """ + } + } + } + + when { + params { + module_args = '-J-Xmx6G --sequenceType DNA' + } process { """ - input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] + def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true ) + def genome_2 = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true ) + + input[0] = [genome_1,genome_2] + input[1] = [] + input[2] = UNZIP_MDB.out.unzipped_archive.map { it[1] } + input[3] = 'mdb' """ } } + + then { + + assertAll( + { assert process.success }, + { assert snapshot( + path("${process.out.index[0]}/index0.idx"), + path("${process.out.index[0]}/ref.db"), + path("${process.out.index[0]}/ref.idx"), + path("${process.out.index[0]}/ref.inf"), + path("${process.out.index[0]}/taxonomy.idx"), + path("${process.out.index[0]}/taxonomy.map"), + path("${process.out.index[0]}/taxonomy.tre"), + process.out.versions + ) + .match() + }, + { assert path(process.out.log[0]).readLines().last().contains("Peak memory") }, + { assert path("${process.out.index[0]}/table0.db").exists() }, + { assert path("${process.out.index[0]}/table0.idx").exists() }, + ) + } } - test("sarscov2 - fastq") { + test("sarscov2 - fastq - abin") { config "./nextflow.config" + + setup { + run("UNZIP", alias: "UNZIP_ABIN") { + script "../../../unzip/main.nf" + process { + """ + input[0] = [[], file("https://software-ab.cs.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true)] + """ + } + } + } + when { params { module_args = '-J-Xmx6G --sequenceType DNA' @@ -34,7 +89,8 @@ nextflow_process { input[0] = [genome_1,genome_2] input[1] = [] - input[2] = UNZIP.out.unzipped_archive.map { it[1] } + input[2] = UNZIP_ABIN.out.unzipped_archive.map { it[1] } + input[3] = 'a2t' """ } } @@ -74,7 +130,8 @@ nextflow_process { input[0] = [genome_1,genome_2] input[1] = [] - input[2] = UNZIP.out.unzipped_archive.map { it[1] } + input[2] = [] + input[3] = 'mdb' """ } } diff --git a/modules/nf-core/malt/build/tests/main.nf.test.snap b/modules/nf-core/malt/build/tests/main.nf.test.snap index 9ff080c8d32..e63f25111ff 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test.snap +++ b/modules/nf-core/malt/build/tests/main.nf.test.snap @@ -1,4 +1,42 @@ { + "sarscov2 - fastq - mdb": { + "content": [ + "index0.idx:md5,0ba3d8bfb7ef28d08e2a005dd3405c55", + "ref.db:md5,6b36ae031c49feaae50f4cea07d9c7f4", + "ref.idx:md5,8ba66cdf65181c7efee1d366574cb9d7", + "ref.inf:md5,042712533a0187b6566db67c6503a71e", + "taxonomy.idx:md5,e7ce35e6238f39fa0c236fcf991546e4", + "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0", + "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e", + [ + "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-04T10:27:03.034359655" + }, + "sarscov2 - fastq - abin": { + "content": [ + "index0.idx:md5,0ba3d8bfb7ef28d08e2a005dd3405c55", + "ref.db:md5,6b0b40df6094a735fa2843e0ef916a02", + "ref.idx:md5,42b0bc56c1562594c7500f2f86a3ca71", + "ref.inf:md5,042712533a0187b6566db67c6503a71e", + "taxonomy.idx:md5,e7ce35e6238f39fa0c236fcf991546e4", + "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0", + "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e", + [ + "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-04T10:30:59.462853239" + }, "sarscov2 - fastq - stub": { "content": [ { @@ -31,24 +69,5 @@ "nextflow": "24.10.0" }, "timestamp": "2024-11-15T12:14:24.942518" - }, - "sarscov2 - fastq": { - "content": [ - "index0.idx:md5,0ba3d8bfb7ef28d08e2a005dd3405c55", - "ref.db:md5,6b36ae031c49feaae50f4cea07d9c7f4", - "ref.idx:md5,8ba66cdf65181c7efee1d366574cb9d7", - "ref.inf:md5,042712533a0187b6566db67c6503a71e", - "taxonomy.idx:md5,e7ce35e6238f39fa0c236fcf991546e4", - "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0", - "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e", - [ - "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.10.0" - }, - "timestamp": "2024-11-15T12:13:59.078459" } } \ No newline at end of file diff --git a/modules/nf-core/malt/build/tests/nextflow.config b/modules/nf-core/malt/build/tests/nextflow.config index f1c7169581e..426bae040de 100644 --- a/modules/nf-core/malt/build/tests/nextflow.config +++ b/modules/nf-core/malt/build/tests/nextflow.config @@ -1,4 +1,8 @@ process { + withName: UNZIP { + ext.prefix = 'mapping_file' + } + withName: MALT_BUILD { ext.args = params.module_args } diff --git a/modules/nf-core/malt/run/environment.yml b/modules/nf-core/malt/run/environment.yml index 15a775008fc..46d86641207 100644 --- a/modules/nf-core/malt/run/environment.yml +++ b/modules/nf-core/malt/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test index a75fe4ee49c..7ccd453fbd0 100644 --- a/modules/nf-core/malt/run/tests/main.nf.test +++ b/modules/nf-core/malt/run/tests/main.nf.test @@ -15,6 +15,7 @@ nextflow_process { setup { run("UNZIP") { script "../../../unzip/main.nf" + config './nextflow.config' process { """ input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] @@ -23,11 +24,13 @@ nextflow_process { } run("MALT_BUILD") { script "../../../malt/build/main.nf" + config './nextflow.config' process { """ input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } + input[3] = 'mdb' """ } } diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 8918381db86..659ce2aa565 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -1,4 +1,7 @@ process { + withName: UNZIP { + ext.prefix = 'mapping_file' + } withName: MALT_BUILD { ext.args = { "-J-Xmx${task.memory.toGiga()}G --sequenceType DNA" } diff --git a/modules/nf-core/maltextract/environment.yml b/modules/nf-core/maltextract/environment.yml index d78219cbe01..a1a3b3a2b2c 100644 --- a/modules/nf-core/maltextract/environment.yml +++ b/modules/nf-core/maltextract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/convertinversion/environment.yml b/modules/nf-core/manta/convertinversion/environment.yml index 802a9f4ddc0..3aa535e8887 100644 --- a/modules/nf-core/manta/convertinversion/environment.yml +++ b/modules/nf-core/manta/convertinversion/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/germline/environment.yml b/modules/nf-core/manta/germline/environment.yml index fe5ade5068f..56c00291a3e 100644 --- a/modules/nf-core/manta/germline/environment.yml +++ b/modules/nf-core/manta/germline/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/somatic/environment.yml b/modules/nf-core/manta/somatic/environment.yml index fe5ade5068f..56c00291a3e 100644 --- a/modules/nf-core/manta/somatic/environment.yml +++ b/modules/nf-core/manta/somatic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/manta/tumoronly/environment.yml b/modules/nf-core/manta/tumoronly/environment.yml index fe5ade5068f..56c00291a3e 100644 --- a/modules/nf-core/manta/tumoronly/environment.yml +++ b/modules/nf-core/manta/tumoronly/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mapad/index/environment.yml b/modules/nf-core/mapad/index/environment.yml index 540878543d1..e8a0291d30f 100644 --- a/modules/nf-core/mapad/index/environment.yml +++ b/modules/nf-core/mapad/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mapad/map/environment.yml b/modules/nf-core/mapad/map/environment.yml index 540878543d1..e8a0291d30f 100644 --- a/modules/nf-core/mapad/map/environment.yml +++ b/modules/nf-core/mapad/map/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mapdamage2/environment.yml b/modules/nf-core/mapdamage2/environment.yml index 2476b31af9a..6891044e5d2 100644 --- a/modules/nf-core/mapdamage2/environment.yml +++ b/modules/nf-core/mapdamage2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mash/dist/environment.yml b/modules/nf-core/mash/dist/environment.yml index 5911571d7fe..0b5e0c44764 100644 --- a/modules/nf-core/mash/dist/environment.yml +++ b/modules/nf-core/mash/dist/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mash/screen/environment.yml b/modules/nf-core/mash/screen/environment.yml index 5911571d7fe..0b5e0c44764 100644 --- a/modules/nf-core/mash/screen/environment.yml +++ b/modules/nf-core/mash/screen/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mash/sketch/environment.yml b/modules/nf-core/mash/sketch/environment.yml index 5911571d7fe..0b5e0c44764 100644 --- a/modules/nf-core/mash/sketch/environment.yml +++ b/modules/nf-core/mash/sketch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mashmap/environment.yml b/modules/nf-core/mashmap/environment.yml index af0aef9d1a1..516b0d31f8d 100644 --- a/modules/nf-core/mashmap/environment.yml +++ b/modules/nf-core/mashmap/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mashmap=3.1.3" + - bioconda::mashmap=3.1.3 diff --git a/modules/nf-core/mashtree/environment.yml b/modules/nf-core/mashtree/environment.yml index 0de7d6108b1..a7aa24aeb14 100644 --- a/modules/nf-core/mashtree/environment.yml +++ b/modules/nf-core/mashtree/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/maxbin2/environment.yml b/modules/nf-core/maxbin2/environment.yml index 8a881999670..2ad8f273e85 100644 --- a/modules/nf-core/maxbin2/environment.yml +++ b/modules/nf-core/maxbin2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 845c8e4ed91..bdb649d3836 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -30,11 +30,13 @@ process MAXBIN2 { def prefix = task.ext.prefix ?: "${meta.id}" if (reads && abund) { error("ERROR: MaxBin2 can only accept one of `reads` or `abund`, no both. Check input.") } def associate_files = "" - if ( reads ) { + if (reads) { associate_files = "-reads $reads" - } else if ( abund instanceof List ) { - associate_files = "-abund ${abund[0]}" - for (i in 2..abund.size()) { associate_files += " -abund$i ${abund[i-1]}" } + } else if (abund instanceof List) { + associate_files = (1..abund.size()).collect { n -> + def arg_n = n == 1 ? "" : "${n}" + return "-abund${arg_n} ${abund[n - 1]}" + }.join(" ") } else { associate_files = "-abund $abund" } @@ -54,4 +56,22 @@ process MAXBIN2 { maxbin2: \$( run_MaxBin.pl -v | head -n 1 | sed 's/MaxBin //' ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if (reads && abund) { error("ERROR: MaxBin2 can only accept one of `reads` or `abund`, no both. Check input.") } + """ + echo "" | gzip > ${prefix}.log.gz + echo "" | gzip > ${prefix}.marker.gz + echo "" | gzip > ${prefix}.marker_of_each_bin.gz + echo "" | gzip > ${prefix}.noclass.gz + touch ${prefix}.summary + echo "" | gzip > ${prefix}.tooshort.gz + echo "" | gzip > ${prefix}.001.fasta.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + maxbin2: \$( run_MaxBin.pl -v | head -n 1 | sed 's/MaxBin //' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/maxbin2/tests/main.nf.test b/modules/nf-core/maxbin2/tests/main.nf.test index efb23c2b159..d51c62097e9 100644 --- a/modules/nf-core/maxbin2/tests/main.nf.test +++ b/modules/nf-core/maxbin2/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "maxbin2" + tag "coverm/contig" test("test-maxbin2") { @@ -44,4 +45,103 @@ nextflow_process { } } + test("test-maxbin2- abund") { + + setup { + run("COVERM_CONTIG") { + script "../../coverm/contig/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [ id:'test2', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) + ] + ] + ) + input[1] = [ + [id: "ref"], + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) + ] + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + ch_coverm_depths = COVERM_CONTIG.out.coverage + .map { meta, coverage -> coverage } + .collect() + .map { coverages -> [ [id: 'ref'], coverages ] } + + input[0] = Channel.of( + [ + [ id: 'ref' ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) + ] + ).combine(ch_coverm_depths, by: 0) + .map { meta, contigs, coverages -> [ meta, contigs, [], coverages ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.binned_fastas, + process.out.summary, + file(process.out.log[0][1]).name, + process.out.marker_counts, + file(process.out.unbinned_fasta[0][1]).name, // empty + process.out.tooshort_fasta, + file(process.out.marker_bins[0][1]).name, // unstable + process.out.marker_genes, + process.out.versions + ).match() + } + ) + } + } + + test("test-maxbin2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test1', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + } diff --git a/modules/nf-core/maxbin2/tests/main.nf.test.snap b/modules/nf-core/maxbin2/tests/main.nf.test.snap index caecef8eea0..2b12f8bc4e7 100644 --- a/modules/nf-core/maxbin2/tests/main.nf.test.snap +++ b/modules/nf-core/maxbin2/tests/main.nf.test.snap @@ -55,5 +55,201 @@ "nextflow": "24.04.4" }, "timestamp": "2024-08-30T14:56:43.557114" + }, + "test-maxbin2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.001.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.log.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.marker.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.noclass.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "6": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.tooshort.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + "versions.yml:md5,a8b5754ee5df020d62ff25306376fc0a" + ], + "abundance": [ + + ], + "binned_fastas": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.001.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "log": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.log.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "marker_bins": [ + + ], + "marker_counts": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.marker.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "marker_genes": [ + + ], + "summary": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tooshort_fasta": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.tooshort.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "unbinned_fasta": [ + [ + { + "id": "test1", + "single_end": false + }, + "test1.noclass.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,a8b5754ee5df020d62ff25306376fc0a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-05T09:39:09.305291376" + }, + "test-maxbin2- abund": { + "content": [ + [ + [ + { + "id": "ref" + }, + [ + "ref.001.fasta.gz:md5,7ff13455c7cc11a5a4967f2fae84e2e9", + "ref.002.fasta.gz:md5,fb0dfa69b9303f1ecca8ce4000706763" + ] + ] + ], + [ + [ + { + "id": "ref" + }, + "ref.summary:md5,9d6c532965630a42ec11cf2f5844e8ca" + ] + ], + "ref.log.gz", + [ + [ + { + "id": "ref" + }, + "ref.marker.gz:md5,8f9853e5ea4bb641bff7c2440178d6bd" + ] + ], + "ref.noclass.gz", + [ + [ + { + "id": "ref" + }, + "ref.tooshort.gz:md5,b4e48e83637217aa9eba7f27f5990b24" + ] + ], + "ref.marker_of_each_bin.tar.gz", + [ + + ], + [ + "versions.yml:md5,a8b5754ee5df020d62ff25306376fc0a" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-05T10:43:41.74526094" } } \ No newline at end of file diff --git a/modules/nf-core/maxquant/lfq/environment.yml b/modules/nf-core/maxquant/lfq/environment.yml index 3344ce5a4e2..24aee2e2cb6 100644 --- a/modules/nf-core/maxquant/lfq/environment.yml +++ b/modules/nf-core/maxquant/lfq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mcroni/environment.yml b/modules/nf-core/mcroni/environment.yml index c20f9a9bd09..f960fd3bfba 100644 --- a/modules/nf-core/mcroni/environment.yml +++ b/modules/nf-core/mcroni/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mcstaging/imc2mc/environment.yml b/modules/nf-core/mcstaging/imc2mc/environment.yml index 238492beb73..11e100f628f 100644 --- a/modules/nf-core/mcstaging/imc2mc/environment.yml +++ b/modules/nf-core/mcstaging/imc2mc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/md5sum/environment.yml b/modules/nf-core/md5sum/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/md5sum/environment.yml +++ b/modules/nf-core/md5sum/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/medaka/environment.yml b/modules/nf-core/medaka/environment.yml index 1165f7c8f7d..23b113cb11d 100644 --- a/modules/nf-core/medaka/environment.yml +++ b/modules/nf-core/medaka/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/megahit/environment.yml b/modules/nf-core/megahit/environment.yml index eed8b725774..1e397251115 100644 --- a/modules/nf-core/megahit/environment.yml +++ b/modules/nf-core/megahit/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/megan/daa2info/environment.yml b/modules/nf-core/megan/daa2info/environment.yml index e31aa147beb..187e1b4890e 100644 --- a/modules/nf-core/megan/daa2info/environment.yml +++ b/modules/nf-core/megan/daa2info/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/megan/rma2info/environment.yml b/modules/nf-core/megan/rma2info/environment.yml index 520b771daab..db327b88a92 100644 --- a/modules/nf-core/megan/rma2info/environment.yml +++ b/modules/nf-core/megan/rma2info/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/meningotype/environment.yml b/modules/nf-core/meningotype/environment.yml index e2f6f59bc79..54d24d8f85c 100644 --- a/modules/nf-core/meningotype/environment.yml +++ b/modules/nf-core/meningotype/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/merfin/hist/environment.yml b/modules/nf-core/merfin/hist/environment.yml index 8a01363ee79..d4d2815e5a0 100644 --- a/modules/nf-core/merfin/hist/environment.yml +++ b/modules/nf-core/merfin/hist/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::merfin=1.0" + - bioconda::merfin=1.0 diff --git a/modules/nf-core/merqury/hapmers/environment.yml b/modules/nf-core/merqury/hapmers/environment.yml index 93a0c984346..84dc78d983b 100644 --- a/modules/nf-core/merqury/hapmers/environment.yml +++ b/modules/nf-core/merqury/hapmers/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::merqury=1.3" + - bioconda::merqury=1.3 diff --git a/modules/nf-core/merqury/merqury/environment.yml b/modules/nf-core/merqury/merqury/environment.yml index a62b4b9200c..84dc78d983b 100644 --- a/modules/nf-core/merqury/merqury/environment.yml +++ b/modules/nf-core/merqury/merqury/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/merquryfk/katcomp/environment.yml b/modules/nf-core/merquryfk/katcomp/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/merquryfk/katcomp/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/merquryfk/katgc/environment.yml b/modules/nf-core/merquryfk/katgc/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/merquryfk/katgc/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/meryl/count/environment.yml b/modules/nf-core/meryl/count/environment.yml index e37d79019af..deebca1f712 100644 --- a/modules/nf-core/meryl/count/environment.yml +++ b/modules/nf-core/meryl/count/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/meryl/histogram/environment.yml b/modules/nf-core/meryl/histogram/environment.yml index e37d79019af..deebca1f712 100644 --- a/modules/nf-core/meryl/histogram/environment.yml +++ b/modules/nf-core/meryl/histogram/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/meryl/unionsum/environment.yml b/modules/nf-core/meryl/unionsum/environment.yml index e37d79019af..deebca1f712 100644 --- a/modules/nf-core/meryl/unionsum/environment.yml +++ b/modules/nf-core/meryl/unionsum/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml index eaa9cbe9325..ba3045e5c26 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metabat2/metabat2/environment.yml b/modules/nf-core/metabat2/metabat2/environment.yml index e411ed8a3bd..57943daa27d 100644 --- a/modules/nf-core/metabat2/metabat2/environment.yml +++ b/modules/nf-core/metabat2/metabat2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metaeuk/easypredict/environment.yml b/modules/nf-core/metaeuk/easypredict/environment.yml index f0543021013..5a9fb7ae87d 100644 --- a/modules/nf-core/metaeuk/easypredict/environment.yml +++ b/modules/nf-core/metaeuk/easypredict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metamaps/classify/environment.yml b/modules/nf-core/metamaps/classify/environment.yml index 18ab06802db..4809b043e35 100644 --- a/modules/nf-core/metamaps/classify/environment.yml +++ b/modules/nf-core/metamaps/classify/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::metamaps=0.1.633d2e0" + - bioconda::metamaps=0.1.633d2e0 diff --git a/modules/nf-core/metamaps/mapdirectly/environment.yml b/modules/nf-core/metamaps/mapdirectly/environment.yml index 18ab06802db..4809b043e35 100644 --- a/modules/nf-core/metamaps/mapdirectly/environment.yml +++ b/modules/nf-core/metamaps/mapdirectly/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::metamaps=0.1.633d2e0" + - bioconda::metamaps=0.1.633d2e0 diff --git a/modules/nf-core/metamdbg/asm/environment.yml b/modules/nf-core/metamdbg/asm/environment.yml index 4c1cd356b7d..5641ddf77c2 100644 --- a/modules/nf-core/metamdbg/asm/environment.yml +++ b/modules/nf-core/metamdbg/asm/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::metamdbg=1.1" + - bioconda::metamdbg=1.1 diff --git a/modules/nf-core/metamdbg/asm/main.nf b/modules/nf-core/metamdbg/asm/main.nf index f421c903307..c258a58e10d 100644 --- a/modules/nf-core/metamdbg/asm/main.nf +++ b/modules/nf-core/metamdbg/asm/main.nf @@ -22,19 +22,15 @@ process METAMDBG_ASM { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - switch(input_type) { - case "hifi": input = "--in-hifi ${reads}"; break - case "ont" : input = "--in-ont ${reads}" ; break - default: - error("ERROR: input_type must be one of either 'hifi' or 'ont'.") - break + if(!(input_type in ["hifi", "ont"])) { + error("ERROR: input_type must be one of either 'hifi' or 'ont'.") } """ metaMDBG asm \\ --threads ${task.cpus} \\ --out-dir . \\ ${args} \\ - ${input} + --in-${input_type} ${reads} rm -r tmp/ diff --git a/modules/nf-core/metaphlan/makedb/environment.yml b/modules/nf-core/metaphlan/makedb/environment.yml index 709ddf70a54..9d800065aaf 100644 --- a/modules/nf-core/metaphlan/makedb/environment.yml +++ b/modules/nf-core/metaphlan/makedb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml b/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml index 709ddf70a54..9d800065aaf 100644 --- a/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml +++ b/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metaphlan/metaphlan/environment.yml b/modules/nf-core/metaphlan/metaphlan/environment.yml index 709ddf70a54..9d800065aaf 100644 --- a/modules/nf-core/metaphlan/metaphlan/environment.yml +++ b/modules/nf-core/metaphlan/metaphlan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml b/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml index 4e44149666c..3350f368dea 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/metaphlan3/metaphlan3/environment.yml b/modules/nf-core/metaphlan3/metaphlan3/environment.yml index 4e44149666c..3350f368dea 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/environment.yml +++ b/modules/nf-core/metaphlan3/metaphlan3/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/methyldackel/extract/environment.yml b/modules/nf-core/methyldackel/extract/environment.yml index 34beddbee52..322e2bb5f6e 100644 --- a/modules/nf-core/methyldackel/extract/environment.yml +++ b/modules/nf-core/methyldackel/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/methyldackel/mbias/environment.yml b/modules/nf-core/methyldackel/mbias/environment.yml index 34beddbee52..322e2bb5f6e 100644 --- a/modules/nf-core/methyldackel/mbias/environment.yml +++ b/modules/nf-core/methyldackel/mbias/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mgikit/demultiplex/environment.yml b/modules/nf-core/mgikit/demultiplex/environment.yml index 9ae214948eb..1e0f192a1e3 100644 --- a/modules/nf-core/mgikit/demultiplex/environment.yml +++ b/modules/nf-core/mgikit/demultiplex/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/midas/run/environment.yml b/modules/nf-core/midas/run/environment.yml index c6b3b735046..d5db5f93a06 100644 --- a/modules/nf-core/midas/run/environment.yml +++ b/modules/nf-core/midas/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mindagap/duplicatefinder/environment.yml b/modules/nf-core/mindagap/duplicatefinder/environment.yml index ac5d6687783..f9b2a1ac752 100644 --- a/modules/nf-core/mindagap/duplicatefinder/environment.yml +++ b/modules/nf-core/mindagap/duplicatefinder/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::mindagap=0.0.2" + - bioconda::mindagap=0.0.2 diff --git a/modules/nf-core/mindagap/mindagap/environment.yml b/modules/nf-core/mindagap/mindagap/environment.yml index 56fd98bf8df..f9b2a1ac752 100644 --- a/modules/nf-core/mindagap/mindagap/environment.yml +++ b/modules/nf-core/mindagap/mindagap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/minia/environment.yml b/modules/nf-core/minia/environment.yml index ff73cbb95e0..42eb2644eef 100644 --- a/modules/nf-core/minia/environment.yml +++ b/modules/nf-core/minia/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/miniasm/environment.yml b/modules/nf-core/miniasm/environment.yml index eeba4d73787..5dd45d626ac 100644 --- a/modules/nf-core/miniasm/environment.yml +++ b/modules/nf-core/miniasm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml index dc6476b721e..60677e6582c 100644 --- a/modules/nf-core/minimap2/align/environment.yml +++ b/modules/nf-core/minimap2/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/minimap2/index/environment.yml b/modules/nf-core/minimap2/index/environment.yml index d1c1b471bec..c2dd2cfd748 100644 --- a/modules/nf-core/minimap2/index/environment.yml +++ b/modules/nf-core/minimap2/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/miniprot/align/environment.yml b/modules/nf-core/miniprot/align/environment.yml index 7e258a047a5..581cccad8d2 100644 --- a/modules/nf-core/miniprot/align/environment.yml +++ b/modules/nf-core/miniprot/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/miniprot/index/environment.yml b/modules/nf-core/miniprot/index/environment.yml index 7e258a047a5..581cccad8d2 100644 --- a/modules/nf-core/miniprot/index/environment.yml +++ b/modules/nf-core/miniprot/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/miranda/environment.yml b/modules/nf-core/miranda/environment.yml index c0053666cc4..cc57c51b764 100644 --- a/modules/nf-core/miranda/environment.yml +++ b/modules/nf-core/miranda/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mirdeep2/mapper/environment.yml b/modules/nf-core/mirdeep2/mapper/environment.yml index fafc6663255..6155b72f9c2 100644 --- a/modules/nf-core/mirdeep2/mapper/environment.yml +++ b/modules/nf-core/mirdeep2/mapper/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirdeep2=2.0.1.2" + - bioconda::mirdeep2=2.0.1.2 diff --git a/modules/nf-core/mirdeep2/mirdeep2/environment.yml b/modules/nf-core/mirdeep2/mirdeep2/environment.yml index fafc6663255..6155b72f9c2 100644 --- a/modules/nf-core/mirdeep2/mirdeep2/environment.yml +++ b/modules/nf-core/mirdeep2/mirdeep2/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirdeep2=2.0.1.2" + - bioconda::mirdeep2=2.0.1.2 diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml index 1f5deb375a8..37e3c08c94c 100644 --- a/modules/nf-core/mirtop/counts/environment.yml +++ b/modules/nf-core/mirtop/counts/environment.yml @@ -4,10 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.28" - - "bioconda::samtools=1.21" - - "conda-forge::python=3.11" - - "conda-forge::biopython=1.83" - - "bioconda::pysam=0.22.1" - - "bioconda::pybedtools=0.10.0" - - "conda-forge::pandas=2.2.2" + - bioconda::mirtop=0.4.28 + - bioconda::pybedtools=0.10.0 + - bioconda::pysam=0.22.1 + - bioconda::samtools=1.21 + - conda-forge::biopython=1.83 + - conda-forge::pandas=2.2.2 + - conda-forge::python=3.11 diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml index 17572707529..37e3c08c94c 100644 --- a/modules/nf-core/mirtop/export/environment.yml +++ b/modules/nf-core/mirtop/export/environment.yml @@ -1,11 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.28" - - "bioconda::samtools=1.21" - - "conda-forge::python=3.11" - - "conda-forge::biopython=1.83" - - "bioconda::pysam=0.22.1" - - "bioconda::pybedtools=0.10.0" - - "conda-forge::pandas=2.2.2" + - bioconda::mirtop=0.4.28 + - bioconda::pybedtools=0.10.0 + - bioconda::pysam=0.22.1 + - bioconda::samtools=1.21 + - conda-forge::biopython=1.83 + - conda-forge::pandas=2.2.2 + - conda-forge::python=3.11 diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml index 1f5deb375a8..37e3c08c94c 100644 --- a/modules/nf-core/mirtop/gff/environment.yml +++ b/modules/nf-core/mirtop/gff/environment.yml @@ -4,10 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.28" - - "bioconda::samtools=1.21" - - "conda-forge::python=3.11" - - "conda-forge::biopython=1.83" - - "bioconda::pysam=0.22.1" - - "bioconda::pybedtools=0.10.0" - - "conda-forge::pandas=2.2.2" + - bioconda::mirtop=0.4.28 + - bioconda::pybedtools=0.10.0 + - bioconda::pysam=0.22.1 + - bioconda::samtools=1.21 + - conda-forge::biopython=1.83 + - conda-forge::pandas=2.2.2 + - conda-forge::python=3.11 diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml index 1f5deb375a8..37e3c08c94c 100644 --- a/modules/nf-core/mirtop/stats/environment.yml +++ b/modules/nf-core/mirtop/stats/environment.yml @@ -4,10 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.28" - - "bioconda::samtools=1.21" - - "conda-forge::python=3.11" - - "conda-forge::biopython=1.83" - - "bioconda::pysam=0.22.1" - - "bioconda::pybedtools=0.10.0" - - "conda-forge::pandas=2.2.2" + - bioconda::mirtop=0.4.28 + - bioconda::pybedtools=0.10.0 + - bioconda::pysam=0.22.1 + - bioconda::samtools=1.21 + - conda-forge::biopython=1.83 + - conda-forge::pandas=2.2.2 + - conda-forge::python=3.11 diff --git a/modules/nf-core/mirtrace/qc/environment.yml b/modules/nf-core/mirtrace/qc/environment.yml index c83822c4dee..0764a1443ca 100644 --- a/modules/nf-core/mirtrace/qc/environment.yml +++ b/modules/nf-core/mirtrace/qc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtrace=1.0.1" + - bioconda::mirtrace=1.0.1 diff --git a/modules/nf-core/mlst/environment.yml b/modules/nf-core/mlst/environment.yml index c0eeb7c80f7..c8e3764dae7 100644 --- a/modules/nf-core/mlst/environment.yml +++ b/modules/nf-core/mlst/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml index c79df337d73..69afa609565 100644 --- a/modules/nf-core/mmseqs/cluster/environment.yml +++ b/modules/nf-core/mmseqs/cluster/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::mmseqs2=17.b804f \ No newline at end of file + - bioconda::mmseqs2=17.b804f diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/createdb/environment.yml +++ b/modules/nf-core/mmseqs/createdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/createindex/environment.yml +++ b/modules/nf-core/mmseqs/createindex/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/createtsv/environment.yml +++ b/modules/nf-core/mmseqs/createtsv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/databases/environment.yml +++ b/modules/nf-core/mmseqs/databases/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/easysearch/environment.yml b/modules/nf-core/mmseqs/easysearch/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/easysearch/environment.yml +++ b/modules/nf-core/mmseqs/easysearch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/linclust/environment.yml +++ b/modules/nf-core/mmseqs/linclust/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/search/environment.yml b/modules/nf-core/mmseqs/search/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/search/environment.yml +++ b/modules/nf-core/mmseqs/search/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml index d3561349025..69afa609565 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mobsuite/recon/environment.yml b/modules/nf-core/mobsuite/recon/environment.yml index 91e0be51014..d6a7ce0e682 100644 --- a/modules/nf-core/mobsuite/recon/environment.yml +++ b/modules/nf-core/mobsuite/recon/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml index 1343a05bbf4..7a87bce9d70 100644 --- a/modules/nf-core/modkit/pileup/environment.yml +++ b/modules/nf-core/modkit/pileup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index bdc4fb5bc94..f871e054e4e 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/motus/downloaddb/environment.yml b/modules/nf-core/motus/downloaddb/environment.yml index 736a527eb44..71d8df57207 100644 --- a/modules/nf-core/motus/downloaddb/environment.yml +++ b/modules/nf-core/motus/downloaddb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/motus/merge/environment.yml b/modules/nf-core/motus/merge/environment.yml index 736a527eb44..71d8df57207 100644 --- a/modules/nf-core/motus/merge/environment.yml +++ b/modules/nf-core/motus/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml index b8ef520eaa2..018b73a24b6 100644 --- a/modules/nf-core/motus/preplong/environment.yml +++ b/modules/nf-core/motus/preplong/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/motus/profile/environment.yml b/modules/nf-core/motus/profile/environment.yml index b8ef520eaa2..018b73a24b6 100644 --- a/modules/nf-core/motus/profile/environment.yml +++ b/modules/nf-core/motus/profile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensor/msi/environment.yml b/modules/nf-core/msisensor/msi/environment.yml index ca813399634..e85bdd6b3a3 100644 --- a/modules/nf-core/msisensor/msi/environment.yml +++ b/modules/nf-core/msisensor/msi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensor/scan/environment.yml b/modules/nf-core/msisensor/scan/environment.yml index ca813399634..e85bdd6b3a3 100644 --- a/modules/nf-core/msisensor/scan/environment.yml +++ b/modules/nf-core/msisensor/scan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensor2/msi/environment.yml b/modules/nf-core/msisensor2/msi/environment.yml index 7f17071a91f..4061123fb9b 100644 --- a/modules/nf-core/msisensor2/msi/environment.yml +++ b/modules/nf-core/msisensor2/msi/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensor2/scan/environment.yml b/modules/nf-core/msisensor2/scan/environment.yml index 7f17071a91f..4061123fb9b 100644 --- a/modules/nf-core/msisensor2/scan/environment.yml +++ b/modules/nf-core/msisensor2/scan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensorpro/msisomatic/environment.yml b/modules/nf-core/msisensorpro/msisomatic/environment.yml index f67b9b733e9..f17216d6c5f 100644 --- a/modules/nf-core/msisensorpro/msisomatic/environment.yml +++ b/modules/nf-core/msisensorpro/msisomatic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/msisensorpro/scan/environment.yml b/modules/nf-core/msisensorpro/scan/environment.yml index f67b9b733e9..f17216d6c5f 100644 --- a/modules/nf-core/msisensorpro/scan/environment.yml +++ b/modules/nf-core/msisensorpro/scan/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mtmalign/align/environment.yml b/modules/nf-core/mtmalign/align/environment.yml index 131c0648d8f..6a4fdc7dddb 100644 --- a/modules/nf-core/mtmalign/align/environment.yml +++ b/modules/nf-core/mtmalign/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mtnucratio/environment.yml b/modules/nf-core/mtnucratio/environment.yml index 3c7cd4b87b5..782caa0ee3a 100644 --- a/modules/nf-core/mtnucratio/environment.yml +++ b/modules/nf-core/mtnucratio/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mudskipper/bulk/environment.yml b/modules/nf-core/mudskipper/bulk/environment.yml index 162b00681c9..34575482614 100644 --- a/modules/nf-core/mudskipper/bulk/environment.yml +++ b/modules/nf-core/mudskipper/bulk/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mudskipper/index/environment.yml b/modules/nf-core/mudskipper/index/environment.yml index 162b00681c9..34575482614 100644 --- a/modules/nf-core/mudskipper/index/environment.yml +++ b/modules/nf-core/mudskipper/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122ce1a6..c3b3413faa6 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/multivcfanalyzer/environment.yml b/modules/nf-core/multivcfanalyzer/environment.yml index 3361a5a4298..add0b883b9c 100644 --- a/modules/nf-core/multivcfanalyzer/environment.yml +++ b/modules/nf-core/multivcfanalyzer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mummer/environment.yml b/modules/nf-core/mummer/environment.yml index 643eff0f740..6ae06e6d995 100644 --- a/modules/nf-core/mummer/environment.yml +++ b/modules/nf-core/mummer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/muscle/environment.yml b/modules/nf-core/muscle/environment.yml index eb0feb4cb55..79c93e64091 100644 --- a/modules/nf-core/muscle/environment.yml +++ b/modules/nf-core/muscle/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/muscle5/super5/environment.yml b/modules/nf-core/muscle5/super5/environment.yml index 3167b845323..b82869d242e 100644 --- a/modules/nf-core/muscle5/super5/environment.yml +++ b/modules/nf-core/muscle5/super5/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/muse/call/environment.yml b/modules/nf-core/muse/call/environment.yml index 5bc34c10360..f81029a392b 100644 --- a/modules/nf-core/muse/call/environment.yml +++ b/modules/nf-core/muse/call/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::muse=2.1.2" + - bioconda::muse=2.1.2 diff --git a/modules/nf-core/muse/sump/environment.yml b/modules/nf-core/muse/sump/environment.yml index 4c481284eae..c8e0bd4a5bb 100644 --- a/modules/nf-core/muse/sump/environment.yml +++ b/modules/nf-core/muse/sump/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::muse=2.1.2 - - bioconda::tabix=1.11 # needed for bgzip + - bioconda::tabix=1.11 diff --git a/modules/nf-core/mygene/environment.yml b/modules/nf-core/mygene/environment.yml index 69dc92378a5..90939eeceb7 100644 --- a/modules/nf-core/mygene/environment.yml +++ b/modules/nf-core/mygene/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/mykrobe/predict/environment.yml b/modules/nf-core/mykrobe/predict/environment.yml index 3d9a6d9c729..d2f57a65827 100644 --- a/modules/nf-core/mykrobe/predict/environment.yml +++ b/modules/nf-core/mykrobe/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nacho/normalize/environment.yml b/modules/nf-core/nacho/normalize/environment.yml index 9cf652c88fe..2e515cb47de 100644 --- a/modules/nf-core/nacho/normalize/environment.yml +++ b/modules/nf-core/nacho/normalize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nacho/qc/environment.yml b/modules/nf-core/nacho/qc/environment.yml index 9cf652c88fe..2e515cb47de 100644 --- a/modules/nf-core/nacho/qc/environment.yml +++ b/modules/nf-core/nacho/qc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nanocomp/environment.yml b/modules/nf-core/nanocomp/environment.yml index dad3490ff8b..f0afc48fe2c 100644 --- a/modules/nf-core/nanocomp/environment.yml +++ b/modules/nf-core/nanocomp/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nanofilt/environment.yml b/modules/nf-core/nanofilt/environment.yml index 497adfdfee6..17e57e84e75 100644 --- a/modules/nf-core/nanofilt/environment.yml +++ b/modules/nf-core/nanofilt/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::nanofilt=2.8.0" + - bioconda::nanofilt=2.8.0 diff --git a/modules/nf-core/nanolyse/environment.yml b/modules/nf-core/nanolyse/environment.yml index 70e4421c5b5..54dc971a839 100644 --- a/modules/nf-core/nanolyse/environment.yml +++ b/modules/nf-core/nanolyse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nanomonsv/parse/environment.yml b/modules/nf-core/nanomonsv/parse/environment.yml index 0311de25eb8..127f423322a 100644 --- a/modules/nf-core/nanomonsv/parse/environment.yml +++ b/modules/nf-core/nanomonsv/parse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nanoplot/environment.yml b/modules/nf-core/nanoplot/environment.yml index 821318c167b..f806e982068 100644 --- a/modules/nf-core/nanoplot/environment.yml +++ b/modules/nf-core/nanoplot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nanoq/environment.yml b/modules/nf-core/nanoq/environment.yml index 1a95d24e4b3..8df81732253 100644 --- a/modules/nf-core/nanoq/environment.yml +++ b/modules/nf-core/nanoq/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::nanoq=0.10.0" + - bioconda::nanoq=0.10.0 diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml index 9a0831a3d28..375823545b9 100644 --- a/modules/nf-core/narfmap/align/environment.yml +++ b/modules/nf-core/narfmap/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/narfmap/hashtable/environment.yml b/modules/nf-core/narfmap/hashtable/environment.yml index 7f169f10b6a..b22a9d55985 100644 --- a/modules/nf-core/narfmap/hashtable/environment.yml +++ b/modules/nf-core/narfmap/hashtable/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ncbigenomedownload/environment.yml b/modules/nf-core/ncbigenomedownload/environment.yml index 7068048d404..80aebf8bdc0 100644 --- a/modules/nf-core/ncbigenomedownload/environment.yml +++ b/modules/nf-core/ncbigenomedownload/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nextclade/datasetget/environment.yml b/modules/nf-core/nextclade/datasetget/environment.yml index 09c0ba1a846..398481e3a70 100644 --- a/modules/nf-core/nextclade/datasetget/environment.yml +++ b/modules/nf-core/nextclade/datasetget/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nextclade/run/environment.yml b/modules/nf-core/nextclade/run/environment.yml index 09c0ba1a846..398481e3a70 100644 --- a/modules/nf-core/nextclade/run/environment.yml +++ b/modules/nf-core/nextclade/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nextgenmap/environment.yml b/modules/nf-core/nextgenmap/environment.yml index 7e7355a83a5..ca2eae15694 100644 --- a/modules/nf-core/nextgenmap/environment.yml +++ b/modules/nf-core/nextgenmap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngmaster/environment.yml b/modules/nf-core/ngmaster/environment.yml index f9405cb4f4e..0e974841855 100644 --- a/modules/nf-core/ngmaster/environment.yml +++ b/modules/nf-core/ngmaster/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::ngmaster=0.5.8 - - conda-forge::python=3.9.7 # Lock from container + - conda-forge::python=3.9.7 diff --git a/modules/nf-core/ngmerge/environment.yml b/modules/nf-core/ngmerge/environment.yml index 2c5ed5437fb..7d578c385f1 100644 --- a/modules/nf-core/ngmerge/environment.yml +++ b/modules/nf-core/ngmerge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml index 98be7c334ec..906277c5dc9 100644 --- a/modules/nf-core/ngsbits/samplegender/environment.yml +++ b/modules/nf-core/ngsbits/samplegender/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngscheckmate/fastq/environment.yml b/modules/nf-core/ngscheckmate/fastq/environment.yml index 117b4e5783b..2efa4fa5a66 100644 --- a/modules/nf-core/ngscheckmate/fastq/environment.yml +++ b/modules/nf-core/ngscheckmate/fastq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngscheckmate/ncm/environment.yml b/modules/nf-core/ngscheckmate/ncm/environment.yml index 117b4e5783b..2efa4fa5a66 100644 --- a/modules/nf-core/ngscheckmate/ncm/environment.yml +++ b/modules/nf-core/ngscheckmate/ncm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngscheckmate/patterngenerator/environment.yml b/modules/nf-core/ngscheckmate/patterngenerator/environment.yml index 117b4e5783b..2efa4fa5a66 100644 --- a/modules/nf-core/ngscheckmate/patterngenerator/environment.yml +++ b/modules/nf-core/ngscheckmate/patterngenerator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ngscheckmate/vafncm/environment.yml b/modules/nf-core/ngscheckmate/vafncm/environment.yml index 117b4e5783b..2efa4fa5a66 100644 --- a/modules/nf-core/ngscheckmate/vafncm/environment.yml +++ b/modules/nf-core/ngscheckmate/vafncm/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nonpareil/curve/environment.yml b/modules/nf-core/nonpareil/curve/environment.yml index 89d5aa6e915..3c98773e5a1 100644 --- a/modules/nf-core/nonpareil/curve/environment.yml +++ b/modules/nf-core/nonpareil/curve/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nonpareil/nonpareil/environment.yml b/modules/nf-core/nonpareil/nonpareil/environment.yml index 89d5aa6e915..3c98773e5a1 100644 --- a/modules/nf-core/nonpareil/nonpareil/environment.yml +++ b/modules/nf-core/nonpareil/nonpareil/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml b/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml index 78bc8437c15..3c98773e5a1 100644 --- a/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml +++ b/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::nonpareil=3.5.5" + - bioconda::nonpareil=3.5.5 diff --git a/modules/nf-core/nonpareil/set/environment.yml b/modules/nf-core/nonpareil/set/environment.yml index 89d5aa6e915..3c98773e5a1 100644 --- a/modules/nf-core/nonpareil/set/environment.yml +++ b/modules/nf-core/nonpareil/set/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/nucmer/environment.yml b/modules/nf-core/nucmer/environment.yml index 643eff0f740..6ae06e6d995 100644 --- a/modules/nf-core/nucmer/environment.yml +++ b/modules/nf-core/nucmer/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/oatk/environment.yml b/modules/nf-core/oatk/environment.yml index 5e5438aac0d..b9ad6895ea1 100644 --- a/modules/nf-core/oatk/environment.yml +++ b/modules/nf-core/oatk/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::oatk=1.0" + - bioconda::oatk=1.0 diff --git a/modules/nf-core/odgi/build/environment.yml b/modules/nf-core/odgi/build/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/build/environment.yml +++ b/modules/nf-core/odgi/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/draw/environment.yml b/modules/nf-core/odgi/draw/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/draw/environment.yml +++ b/modules/nf-core/odgi/draw/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/layout/environment.yml b/modules/nf-core/odgi/layout/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/layout/environment.yml +++ b/modules/nf-core/odgi/layout/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/sort/environment.yml b/modules/nf-core/odgi/sort/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/sort/environment.yml +++ b/modules/nf-core/odgi/sort/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/squeeze/environment.yml b/modules/nf-core/odgi/squeeze/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/squeeze/environment.yml +++ b/modules/nf-core/odgi/squeeze/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/stats/environment.yml b/modules/nf-core/odgi/stats/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/stats/environment.yml +++ b/modules/nf-core/odgi/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/unchop/environment.yml b/modules/nf-core/odgi/unchop/environment.yml index 9e850ef1c78..ea100ec9957 100644 --- a/modules/nf-core/odgi/unchop/environment.yml +++ b/modules/nf-core/odgi/unchop/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.9.0 \ No newline at end of file + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/view/environment.yml b/modules/nf-core/odgi/view/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/view/environment.yml +++ b/modules/nf-core/odgi/view/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/odgi/viz/environment.yml b/modules/nf-core/odgi/viz/environment.yml index ecfae63b909..ea100ec9957 100644 --- a/modules/nf-core/odgi/viz/environment.yml +++ b/modules/nf-core/odgi/viz/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/oncocnv/environment.yml b/modules/nf-core/oncocnv/environment.yml index 97fc9a5446c..6689359662b 100644 --- a/modules/nf-core/oncocnv/environment.yml +++ b/modules/nf-core/oncocnv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/openms/decoydatabase/environment.yml b/modules/nf-core/openms/decoydatabase/environment.yml index 31614292dbe..eb830c433b7 100644 --- a/modules/nf-core/openms/decoydatabase/environment.yml +++ b/modules/nf-core/openms/decoydatabase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/openms/filefilter/environment.yml b/modules/nf-core/openms/filefilter/environment.yml index 5ec74436391..eb830c433b7 100644 --- a/modules/nf-core/openms/filefilter/environment.yml +++ b/modules/nf-core/openms/filefilter/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/idfilter/environment.yml b/modules/nf-core/openms/idfilter/environment.yml index 5ec74436391..eb830c433b7 100644 --- a/modules/nf-core/openms/idfilter/environment.yml +++ b/modules/nf-core/openms/idfilter/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/idmassaccuracy/environment.yml b/modules/nf-core/openms/idmassaccuracy/environment.yml index 5ec74436391..eb830c433b7 100644 --- a/modules/nf-core/openms/idmassaccuracy/environment.yml +++ b/modules/nf-core/openms/idmassaccuracy/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/idmerger/environment.yml b/modules/nf-core/openms/idmerger/environment.yml index 31614292dbe..eb830c433b7 100644 --- a/modules/nf-core/openms/idmerger/environment.yml +++ b/modules/nf-core/openms/idmerger/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/openms/idripper/environment.yml b/modules/nf-core/openms/idripper/environment.yml index 5ec74436391..eb830c433b7 100644 --- a/modules/nf-core/openms/idripper/environment.yml +++ b/modules/nf-core/openms/idripper/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/idscoreswitcher/environment.yml b/modules/nf-core/openms/idscoreswitcher/environment.yml index 5ec74436391..eb830c433b7 100644 --- a/modules/nf-core/openms/idscoreswitcher/environment.yml +++ b/modules/nf-core/openms/idscoreswitcher/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/peakpickerhires/environment.yml b/modules/nf-core/openms/peakpickerhires/environment.yml index d4d40e896b1..eb830c433b7 100644 --- a/modules/nf-core/openms/peakpickerhires/environment.yml +++ b/modules/nf-core/openms/peakpickerhires/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/peptideindexer/environment.yml b/modules/nf-core/openms/peptideindexer/environment.yml index d6e51812af3..eb830c433b7 100644 --- a/modules/nf-core/openms/peptideindexer/environment.yml +++ b/modules/nf-core/openms/peptideindexer/environment.yml @@ -1,6 +1,7 @@ --- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.2.0" + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml index dfc10603608..d288c5e471b 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml +++ b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::openms-thirdparty=3.2.0" + - bioconda::openms-thirdparty=3.2.0 diff --git a/modules/nf-core/optitype/environment.yml b/modules/nf-core/optitype/environment.yml index add1d36c65f..55b01e98efc 100644 --- a/modules/nf-core/optitype/environment.yml +++ b/modules/nf-core/optitype/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml index 68c475f8ddb..7696be75a0c 100644 --- a/modules/nf-core/orthofinder/environment.yml +++ b/modules/nf-core/orthofinder/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/paftools/sam2paf/environment.yml b/modules/nf-core/paftools/sam2paf/environment.yml index 988733dd5c5..ca0563e98ce 100644 --- a/modules/nf-core/paftools/sam2paf/environment.yml +++ b/modules/nf-core/paftools/sam2paf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairix/environment.yml b/modules/nf-core/pairix/environment.yml index d544ae499c2..a41df61cccc 100644 --- a/modules/nf-core/pairix/environment.yml +++ b/modules/nf-core/pairix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/dedup/environment.yml b/modules/nf-core/pairtools/dedup/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/dedup/environment.yml +++ b/modules/nf-core/pairtools/dedup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/flip/environment.yml b/modules/nf-core/pairtools/flip/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/flip/environment.yml +++ b/modules/nf-core/pairtools/flip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/merge/environment.yml b/modules/nf-core/pairtools/merge/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/merge/environment.yml +++ b/modules/nf-core/pairtools/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/parse/environment.yml b/modules/nf-core/pairtools/parse/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/parse/environment.yml +++ b/modules/nf-core/pairtools/parse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/restrict/environment.yml b/modules/nf-core/pairtools/restrict/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/restrict/environment.yml +++ b/modules/nf-core/pairtools/restrict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/select/environment.yml b/modules/nf-core/pairtools/select/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/select/environment.yml +++ b/modules/nf-core/pairtools/select/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/sort/environment.yml b/modules/nf-core/pairtools/sort/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/sort/environment.yml +++ b/modules/nf-core/pairtools/sort/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/split/environment.yml b/modules/nf-core/pairtools/split/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/split/environment.yml +++ b/modules/nf-core/pairtools/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pairtools/stats/environment.yml b/modules/nf-core/pairtools/stats/environment.yml index e88acbcd0c5..d2523556961 100644 --- a/modules/nf-core/pairtools/stats/environment.yml +++ b/modules/nf-core/pairtools/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/panacus/histgrowth/environment.yml b/modules/nf-core/panacus/histgrowth/environment.yml index f08d28e1cac..b50ce525e8f 100644 --- a/modules/nf-core/panacus/histgrowth/environment.yml +++ b/modules/nf-core/panacus/histgrowth/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::panacus=0.2.3" + - bioconda::panacus=0.2.3 diff --git a/modules/nf-core/panacus/visualize/environment.yml b/modules/nf-core/panacus/visualize/environment.yml index f08d28e1cac..b50ce525e8f 100644 --- a/modules/nf-core/panacus/visualize/environment.yml +++ b/modules/nf-core/panacus/visualize/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::panacus=0.2.3" + - bioconda::panacus=0.2.3 diff --git a/modules/nf-core/panaroo/run/environment.yml b/modules/nf-core/panaroo/run/environment.yml index a2de1fe403b..15ee50c9f9c 100644 --- a/modules/nf-core/panaroo/run/environment.yml +++ b/modules/nf-core/panaroo/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pangolin/run/environment.yml b/modules/nf-core/pangolin/run/environment.yml index d4379368c85..2858d5f909e 100644 --- a/modules/nf-core/pangolin/run/environment.yml +++ b/modules/nf-core/pangolin/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pangolin/updatedata/environment.yml b/modules/nf-core/pangolin/updatedata/environment.yml index d4379368c85..2858d5f909e 100644 --- a/modules/nf-core/pangolin/updatedata/environment.yml +++ b/modules/nf-core/pangolin/updatedata/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml index 3bf25c6832f..4bb2afc1aa4 100644 --- a/modules/nf-core/parabricks/applybqsr/meta.yml +++ b/modules/nf-core/parabricks/applybqsr/meta.yml @@ -88,4 +88,4 @@ authors: - "@bsiranosian" maintainers: - "@bsiranosian" - - "@famosab" \ No newline at end of file + - "@famosab" diff --git a/modules/nf-core/parabricks/dbsnp/meta.yml b/modules/nf-core/parabricks/dbsnp/meta.yml index fe363cdecf8..80c0293f984 100644 --- a/modules/nf-core/parabricks/dbsnp/meta.yml +++ b/modules/nf-core/parabricks/dbsnp/meta.yml @@ -51,4 +51,4 @@ output: authors: - "@Furentsu" maintainers: - - "@famosab" \ No newline at end of file + - "@famosab" diff --git a/modules/nf-core/parabricks/deepvariant/meta.yml b/modules/nf-core/parabricks/deepvariant/meta.yml index 21a55a47ef0..3f21b0a30b1 100644 --- a/modules/nf-core/parabricks/deepvariant/meta.yml +++ b/modules/nf-core/parabricks/deepvariant/meta.yml @@ -56,7 +56,7 @@ output: description: vcf file created with deepvariant (does not support .gz for normal vcf), optional pattern: "*.vcf" - gvcf: - - meta: + - meta: type: map description: | Groovy Map containing sample information. diff --git a/modules/nf-core/parabricks/genotypegvcf/meta.yml b/modules/nf-core/parabricks/genotypegvcf/meta.yml index a044fa88795..d0e2a70a740 100644 --- a/modules/nf-core/parabricks/genotypegvcf/meta.yml +++ b/modules/nf-core/parabricks/genotypegvcf/meta.yml @@ -54,4 +54,4 @@ authors: - "@Furentsu" - "@bsiranosian" maintainers: - - "@famosab" \ No newline at end of file + - "@famosab" diff --git a/modules/nf-core/parabricks/indexgvcf/meta.yml b/modules/nf-core/parabricks/indexgvcf/meta.yml index 16834c645d6..ff5a1bde1b2 100644 --- a/modules/nf-core/parabricks/indexgvcf/meta.yml +++ b/modules/nf-core/parabricks/indexgvcf/meta.yml @@ -45,4 +45,4 @@ authors: - "@Furentsu" - "@bsiranosian" maintainers: - - "@famosab" \ No newline at end of file + - "@famosab" diff --git a/modules/nf-core/parabricks/mutectcaller/meta.yml b/modules/nf-core/parabricks/mutectcaller/meta.yml index 4e67686989a..b029b63e400 100644 --- a/modules/nf-core/parabricks/mutectcaller/meta.yml +++ b/modules/nf-core/parabricks/mutectcaller/meta.yml @@ -91,4 +91,4 @@ output: authors: - "@bsiranosian" maintainers: - - "@famosab" \ No newline at end of file + - "@famosab" diff --git a/modules/nf-core/paraclu/environment.yml b/modules/nf-core/paraclu/environment.yml index 505ec1b49b9..afdba47a2dd 100644 --- a/modules/nf-core/paraclu/environment.yml +++ b/modules/nf-core/paraclu/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/paragraph/idxdepth/environment.yml b/modules/nf-core/paragraph/idxdepth/environment.yml index e0718a75867..eeb8cddc6c6 100644 --- a/modules/nf-core/paragraph/idxdepth/environment.yml +++ b/modules/nf-core/paragraph/idxdepth/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/paragraph/multigrmpy/environment.yml b/modules/nf-core/paragraph/multigrmpy/environment.yml index e0718a75867..eeb8cddc6c6 100644 --- a/modules/nf-core/paragraph/multigrmpy/environment.yml +++ b/modules/nf-core/paragraph/multigrmpy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/paragraph/vcf2paragraph/environment.yml b/modules/nf-core/paragraph/vcf2paragraph/environment.yml index ced1599f3d0..f0335f60884 100644 --- a/modules/nf-core/paragraph/vcf2paragraph/environment.yml +++ b/modules/nf-core/paragraph/vcf2paragraph/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml index 0e5a632ebfa..dbdc4262e23 100644 --- a/modules/nf-core/paraphase/environment.yml +++ b/modules/nf-core/paraphase/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pasty/environment.yml b/modules/nf-core/pasty/environment.yml index 2992999068a..f882d0e0ec6 100644 --- a/modules/nf-core/pasty/environment.yml +++ b/modules/nf-core/pasty/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pbbam/pbmerge/environment.yml b/modules/nf-core/pbbam/pbmerge/environment.yml index 7d11d83d698..62ea7afedeb 100644 --- a/modules/nf-core/pbbam/pbmerge/environment.yml +++ b/modules/nf-core/pbbam/pbmerge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pbccs/environment.yml b/modules/nf-core/pbccs/environment.yml index 7801a4fd848..6502384978b 100644 --- a/modules/nf-core/pbccs/environment.yml +++ b/modules/nf-core/pbccs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pbmm2/align/environment.yml b/modules/nf-core/pbmm2/align/environment.yml index 241a59c7501..53cf1c170fd 100644 --- a/modules/nf-core/pbmm2/align/environment.yml +++ b/modules/nf-core/pbmm2/align/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbmm2=1.14.99" + - bioconda::pbmm2=1.14.99 diff --git a/modules/nf-core/pbptyper/environment.yml b/modules/nf-core/pbptyper/environment.yml index bc43f54a8d7..1349f49ba7d 100644 --- a/modules/nf-core/pbptyper/environment.yml +++ b/modules/nf-core/pbptyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pbsv/call/environment.yml b/modules/nf-core/pbsv/call/environment.yml index a48d2440108..a0649adc56c 100644 --- a/modules/nf-core/pbsv/call/environment.yml +++ b/modules/nf-core/pbsv/call/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbsv=2.9.0" + - bioconda::pbsv=2.9.0 diff --git a/modules/nf-core/pbsv/discover/environment.yml b/modules/nf-core/pbsv/discover/environment.yml index a48d2440108..a0649adc56c 100644 --- a/modules/nf-core/pbsv/discover/environment.yml +++ b/modules/nf-core/pbsv/discover/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbsv=2.9.0" + - bioconda::pbsv=2.9.0 diff --git a/modules/nf-core/pbtk/pbindex/environment.yml b/modules/nf-core/pbtk/pbindex/environment.yml index e208868ba9e..38649e1fd0d 100644 --- a/modules/nf-core/pbtk/pbindex/environment.yml +++ b/modules/nf-core/pbtk/pbindex/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbtk=3.1.1" + - bioconda::pbtk=3.1.1 diff --git a/modules/nf-core/pear/environment.yml b/modules/nf-core/pear/environment.yml index c0908a54eb2..749de05f72f 100644 --- a/modules/nf-core/pear/environment.yml +++ b/modules/nf-core/pear/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/peddy/environment.yml b/modules/nf-core/peddy/environment.yml index 8d7fa2b6ac2..2bb1deb8ee0 100644 --- a/modules/nf-core/peddy/environment.yml +++ b/modules/nf-core/peddy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/peka/environment.yml b/modules/nf-core/peka/environment.yml index 2aaf62b2f68..28c52d4b706 100644 --- a/modules/nf-core/peka/environment.yml +++ b/modules/nf-core/peka/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml index 8967e158aad..4eb7d888719 100644 --- a/modules/nf-core/phantompeakqualtools/environment.yml +++ b/modules/nf-core/phantompeakqualtools/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::phantompeakqualtools=1.2.2" + - bioconda::phantompeakqualtools=1.2.2 diff --git a/modules/nf-core/pharokka/installdatabases/environment.yml b/modules/nf-core/pharokka/installdatabases/environment.yml index 2c0e6a0f03c..ca0dcf602f1 100644 --- a/modules/nf-core/pharokka/installdatabases/environment.yml +++ b/modules/nf-core/pharokka/installdatabases/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pharokka=1.7.3" + - bioconda::pharokka=1.7.3 diff --git a/modules/nf-core/pharokka/pharokka/environment.yml b/modules/nf-core/pharokka/pharokka/environment.yml index 2c0e6a0f03c..ca0dcf602f1 100644 --- a/modules/nf-core/pharokka/pharokka/environment.yml +++ b/modules/nf-core/pharokka/pharokka/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pharokka=1.7.3" + - bioconda::pharokka=1.7.3 diff --git a/modules/nf-core/phispy/environment.yml b/modules/nf-core/phispy/environment.yml index 6b1821934dd..77012cbd38b 100644 --- a/modules/nf-core/phispy/environment.yml +++ b/modules/nf-core/phispy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml index 2ebb5e261a1..a094ac54d60 100644 --- a/modules/nf-core/phyloflash/environment.yml +++ b/modules/nf-core/phyloflash/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/bedtointervallist/environment.yml +++ b/modules/nf-core/picard/bedtointervallist/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/cleansam/environment.yml +++ b/modules/nf-core/picard/cleansam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 13265842fcf..5f2dfc0316b 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/createsequencedictionary/environment.yml +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/extractfingerprint/environment.yml +++ b/modules/nf-core/picard/extractfingerprint/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/fastqtosam/environment.yml +++ b/modules/nf-core/picard/fastqtosam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/filtersamreads/environment.yml +++ b/modules/nf-core/picard/filtersamreads/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/fixmateinformation/environment.yml +++ b/modules/nf-core/picard/fixmateinformation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/mergesamfiles/environment.yml +++ b/modules/nf-core/picard/mergesamfiles/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml b/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml index 5f919a9a9b5..b2231a73c21 100644 --- a/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml +++ b/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/sortsam/environment.yml +++ b/modules/nf-core/picard/sortsam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index 1d715d564e9..8f34e975c59 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pigz/compress/environment.yml b/modules/nf-core/pigz/compress/environment.yml index 5016d22697d..a91b6f426b0 100644 --- a/modules/nf-core/pigz/compress/environment.yml +++ b/modules/nf-core/pigz/compress/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "pigz=2.8" + - pigz=2.8 diff --git a/modules/nf-core/pilon/environment.yml b/modules/nf-core/pilon/environment.yml index a67d286906e..eca24d42ce3 100644 --- a/modules/nf-core/pilon/environment.yml +++ b/modules/nf-core/pilon/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pindel/pindel/environment.yml b/modules/nf-core/pindel/pindel/environment.yml index 0941ad7feb2..409d4384f19 100644 --- a/modules/nf-core/pindel/pindel/environment.yml +++ b/modules/nf-core/pindel/pindel/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pints/caller/environment.yml b/modules/nf-core/pints/caller/environment.yml index 1c29653cc0a..b3c957adcd2 100644 --- a/modules/nf-core/pints/caller/environment.yml +++ b/modules/nf-core/pints/caller/environment.yml @@ -1,11 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - pybedtools - bedtools - htslib - pip + - pybedtools - pip: # FIXME https://github.com/nf-core/modules/issues/5814 # NOTE PINTS isn't adding conda builds and is a few versions behind. # renovate: datasource=pypi depName=pypints diff --git a/modules/nf-core/pirate/environment.yml b/modules/nf-core/pirate/environment.yml index 4a770adcbef..70b6e576daf 100644 --- a/modules/nf-core/pirate/environment.yml +++ b/modules/nf-core/pirate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plasmidfinder/environment.yml b/modules/nf-core/plasmidfinder/environment.yml index f38092872c1..0e80de1b24e 100644 --- a/modules/nf-core/plasmidfinder/environment.yml +++ b/modules/nf-core/plasmidfinder/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plasmidid/environment.yml b/modules/nf-core/plasmidid/environment.yml index 173c247532c..dd0f4a649fa 100644 --- a/modules/nf-core/plasmidid/environment.yml +++ b/modules/nf-core/plasmidid/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/platypus/environment.yml b/modules/nf-core/platypus/environment.yml index 39bd8ad6325..000951e59d6 100644 --- a/modules/nf-core/platypus/environment.yml +++ b/modules/nf-core/platypus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/bcf/environment.yml b/modules/nf-core/plink/bcf/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/bcf/environment.yml +++ b/modules/nf-core/plink/bcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/epistasis/environment.yml b/modules/nf-core/plink/epistasis/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/epistasis/environment.yml +++ b/modules/nf-core/plink/epistasis/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/exclude/environment.yml b/modules/nf-core/plink/exclude/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/exclude/environment.yml +++ b/modules/nf-core/plink/exclude/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/extract/environment.yml b/modules/nf-core/plink/extract/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/extract/environment.yml +++ b/modules/nf-core/plink/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/fastepistasis/environment.yml b/modules/nf-core/plink/fastepistasis/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/fastepistasis/environment.yml +++ b/modules/nf-core/plink/fastepistasis/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/genome/environment.yml b/modules/nf-core/plink/genome/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/genome/environment.yml +++ b/modules/nf-core/plink/genome/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/gwas/environment.yml b/modules/nf-core/plink/gwas/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/gwas/environment.yml +++ b/modules/nf-core/plink/gwas/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/hwe/environment.yml b/modules/nf-core/plink/hwe/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/hwe/environment.yml +++ b/modules/nf-core/plink/hwe/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/indep/environment.yml b/modules/nf-core/plink/indep/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/indep/environment.yml +++ b/modules/nf-core/plink/indep/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/indeppairwise/environment.yml b/modules/nf-core/plink/indeppairwise/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/indeppairwise/environment.yml +++ b/modules/nf-core/plink/indeppairwise/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/ld/environment.yml b/modules/nf-core/plink/ld/environment.yml index dbc6dbb3349..fe7bb86b08c 100644 --- a/modules/nf-core/plink/ld/environment.yml +++ b/modules/nf-core/plink/ld/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::plink=1.90b6.21" + - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/recode/environment.yml b/modules/nf-core/plink/recode/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/recode/environment.yml +++ b/modules/nf-core/plink/recode/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink/vcf/environment.yml b/modules/nf-core/plink/vcf/environment.yml index d860c8337c7..fe7bb86b08c 100644 --- a/modules/nf-core/plink/vcf/environment.yml +++ b/modules/nf-core/plink/vcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink2/extract/environment.yml b/modules/nf-core/plink2/extract/environment.yml index b0a71e149e0..1af072c31f3 100644 --- a/modules/nf-core/plink2/extract/environment.yml +++ b/modules/nf-core/plink2/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink2/score/environment.yml b/modules/nf-core/plink2/score/environment.yml index b0a71e149e0..1af072c31f3 100644 --- a/modules/nf-core/plink2/score/environment.yml +++ b/modules/nf-core/plink2/score/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/plink2/vcf/environment.yml b/modules/nf-core/plink2/vcf/environment.yml index b0a71e149e0..1af072c31f3 100644 --- a/modules/nf-core/plink2/vcf/environment.yml +++ b/modules/nf-core/plink2/vcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pmdtools/filter/environment.yml b/modules/nf-core/pmdtools/filter/environment.yml index efbb77ebd11..056c22dd7e6 100644 --- a/modules/nf-core/pmdtools/filter/environment.yml +++ b/modules/nf-core/pmdtools/filter/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::pmdtools=0.60 - - bioconda::samtools=1.14 # Version lock with container + - bioconda::samtools=1.14 diff --git a/modules/nf-core/pneumocat/environment.yml b/modules/nf-core/pneumocat/environment.yml index 55fec0f5d48..a1c1e78ca4c 100644 --- a/modules/nf-core/pneumocat/environment.yml +++ b/modules/nf-core/pneumocat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/poolsnp/environment.yml b/modules/nf-core/poolsnp/environment.yml index 489d578f266..6cbe50b3123 100644 --- a/modules/nf-core/poolsnp/environment.yml +++ b/modules/nf-core/poolsnp/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::poolsnp=1.0.1" + - bioconda::poolsnp=1.0.1 diff --git a/modules/nf-core/popscle/demuxlet/environment.yml b/modules/nf-core/popscle/demuxlet/environment.yml index 555c9debb1b..1fe132c2fa8 100644 --- a/modules/nf-core/popscle/demuxlet/environment.yml +++ b/modules/nf-core/popscle/demuxlet/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::popscle=0.1" + - bioconda::popscle=0.1 diff --git a/modules/nf-core/popscle/dscpileup/environment.yml b/modules/nf-core/popscle/dscpileup/environment.yml index 555c9debb1b..1fe132c2fa8 100644 --- a/modules/nf-core/popscle/dscpileup/environment.yml +++ b/modules/nf-core/popscle/dscpileup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::popscle=0.1" + - bioconda::popscle=0.1 diff --git a/modules/nf-core/popscle/freemuxlet/environment.yml b/modules/nf-core/popscle/freemuxlet/environment.yml index 555c9debb1b..1fe132c2fa8 100644 --- a/modules/nf-core/popscle/freemuxlet/environment.yml +++ b/modules/nf-core/popscle/freemuxlet/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::popscle=0.1" + - bioconda::popscle=0.1 diff --git a/modules/nf-core/porechop/porechop/environment.yml b/modules/nf-core/porechop/porechop/environment.yml index 4defeb33513..b2696aeddff 100644 --- a/modules/nf-core/porechop/porechop/environment.yml +++ b/modules/nf-core/porechop/porechop/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/preseq/ccurve/environment.yml b/modules/nf-core/preseq/ccurve/environment.yml index 6300d3f33a8..a2088502826 100644 --- a/modules/nf-core/preseq/ccurve/environment.yml +++ b/modules/nf-core/preseq/ccurve/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 6300d3f33a8..a2088502826 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/presto/filterseq/environment.yml b/modules/nf-core/presto/filterseq/environment.yml index 8896f444ba6..8f892e149aa 100644 --- a/modules/nf-core/presto/filterseq/environment.yml +++ b/modules/nf-core/presto/filterseq/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::presto=0.7.1" + - bioconda::presto=0.7.1 diff --git a/modules/nf-core/pretextmap/environment.yml b/modules/nf-core/pretextmap/environment.yml index bfbbee2b72f..87c9a1fd0cf 100644 --- a/modules/nf-core/pretextmap/environment.yml +++ b/modules/nf-core/pretextmap/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pretextsnapshot/environment.yml b/modules/nf-core/pretextsnapshot/environment.yml index ed721522641..c275e6ad0e9 100644 --- a/modules/nf-core/pretextsnapshot/environment.yml +++ b/modules/nf-core/pretextsnapshot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/prinseqplusplus/environment.yml b/modules/nf-core/prinseqplusplus/environment.yml index fe598ef114e..4656e948538 100644 --- a/modules/nf-core/prinseqplusplus/environment.yml +++ b/modules/nf-core/prinseqplusplus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml index 7609bf3bd16..b2c7efcf64c 100644 --- a/modules/nf-core/prodigal/environment.yml +++ b/modules/nf-core/prodigal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml index 1d1a019f726..b4687037b10 100644 --- a/modules/nf-core/prokka/environment.yml +++ b/modules/nf-core/prokka/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/proovframe/fix/environment.yml b/modules/nf-core/proovframe/fix/environment.yml index a1a698f477b..d4c7a895a6d 100644 --- a/modules/nf-core/proovframe/fix/environment.yml +++ b/modules/nf-core/proovframe/fix/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::proovframe=0.9.7" + - bioconda::proovframe=0.9.7 diff --git a/modules/nf-core/proovframe/map/environment.yml b/modules/nf-core/proovframe/map/environment.yml index a1a698f477b..d4c7a895a6d 100644 --- a/modules/nf-core/proovframe/map/environment.yml +++ b/modules/nf-core/proovframe/map/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::proovframe=0.9.7" + - bioconda::proovframe=0.9.7 diff --git a/modules/nf-core/propr/grea/environment.yml b/modules/nf-core/propr/grea/environment.yml index 9744dab906b..f6cf0b7154e 100644 --- a/modules/nf-core/propr/grea/environment.yml +++ b/modules/nf-core/propr/grea/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/propr/logratio/environment.yml b/modules/nf-core/propr/logratio/environment.yml index 7064f1712b4..4ba3fd41223 100644 --- a/modules/nf-core/propr/logratio/environment.yml +++ b/modules/nf-core/propr/logratio/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/propr/propd/environment.yml b/modules/nf-core/propr/propd/environment.yml index 9744dab906b..f6cf0b7154e 100644 --- a/modules/nf-core/propr/propd/environment.yml +++ b/modules/nf-core/propr/propd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/propr/propr/environment.yml b/modules/nf-core/propr/propr/environment.yml index f7da56ebc39..4ed7d1b2e65 100644 --- a/modules/nf-core/propr/propr/environment.yml +++ b/modules/nf-core/propr/propr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/proteinortho/environment.yml b/modules/nf-core/proteinortho/environment.yml index d4ca9e72fc1..648ddba6ae5 100644 --- a/modules/nf-core/proteinortho/environment.yml +++ b/modules/nf-core/proteinortho/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/proteus/readproteingroups/environment.yml b/modules/nf-core/proteus/readproteingroups/environment.yml index 986db59603a..2d35012a149 100644 --- a/modules/nf-core/proteus/readproteingroups/environment.yml +++ b/modules/nf-core/proteus/readproteingroups/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pureclip/environment.yml b/modules/nf-core/pureclip/environment.yml index 2bea248a17a..303778c9a6e 100644 --- a/modules/nf-core/pureclip/environment.yml +++ b/modules/nf-core/pureclip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purecn/coverage/environment.yml b/modules/nf-core/purecn/coverage/environment.yml index ffb69fe35cc..314d904e879 100644 --- a/modules/nf-core/purecn/coverage/environment.yml +++ b/modules/nf-core/purecn/coverage/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purecn/intervalfile/environment.yml b/modules/nf-core/purecn/intervalfile/environment.yml index 9717427ab5d..96c91b494e1 100644 --- a/modules/nf-core/purecn/intervalfile/environment.yml +++ b/modules/nf-core/purecn/intervalfile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purecn/normaldb/environment.yml b/modules/nf-core/purecn/normaldb/environment.yml index 9717427ab5d..96c91b494e1 100644 --- a/modules/nf-core/purecn/normaldb/environment.yml +++ b/modules/nf-core/purecn/normaldb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purecn/run/environment.yml b/modules/nf-core/purecn/run/environment.yml index ffb69fe35cc..314d904e879 100644 --- a/modules/nf-core/purecn/run/environment.yml +++ b/modules/nf-core/purecn/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/calcuts/environment.yml b/modules/nf-core/purgedups/calcuts/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/calcuts/environment.yml +++ b/modules/nf-core/purgedups/calcuts/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/getseqs/environment.yml b/modules/nf-core/purgedups/getseqs/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/getseqs/environment.yml +++ b/modules/nf-core/purgedups/getseqs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/histplot/environment.yml b/modules/nf-core/purgedups/histplot/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/histplot/environment.yml +++ b/modules/nf-core/purgedups/histplot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/pbcstat/environment.yml b/modules/nf-core/purgedups/pbcstat/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/pbcstat/environment.yml +++ b/modules/nf-core/purgedups/pbcstat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/purgedups/environment.yml b/modules/nf-core/purgedups/purgedups/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/purgedups/environment.yml +++ b/modules/nf-core/purgedups/purgedups/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/purgedups/splitfa/environment.yml b/modules/nf-core/purgedups/splitfa/environment.yml index 8c4861fa61a..eaeed2c0ecf 100644 --- a/modules/nf-core/purgedups/splitfa/environment.yml +++ b/modules/nf-core/purgedups/splitfa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pychopper/environment.yml b/modules/nf-core/pychopper/environment.yml new file mode 100644 index 00000000000..6b530615c1b --- /dev/null +++ b/modules/nf-core/pychopper/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::pychopper=2.7.10" diff --git a/modules/nf-core/pychopper/main.nf b/modules/nf-core/pychopper/main.nf new file mode 100644 index 00000000000..dea2d0f0d6e --- /dev/null +++ b/modules/nf-core/pychopper/main.nf @@ -0,0 +1,52 @@ +process PYCHOPPER { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pychopper:2.7.10--pyhdfd78af_0': + 'biocontainers/pychopper:2.7.10--pyhdfd78af_0' }" + + input: + tuple val(meta), path(fastq) + + output: + tuple val(meta), path("*.out.fastq.gz"), emit: fastq + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def PYCHOPPER_VERSION = '2.7.10' + + """ + pychopper \\ + $args \\ + -t $task.cpus \\ + $fastq \\ + ${prefix}.out.fastq + + gzip -f ${prefix}.out.fastq > ${prefix}.out.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pychopper: $PYCHOPPER_VERSION (hard coded- check container used for this module) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.out.fastq + gzip ${prefix}.out.fastq + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pychopper: 2.7.10 (hard coded- check container used for this module) + END_VERSIONS + """ +} diff --git a/modules/nf-core/pychopper/meta.yml b/modules/nf-core/pychopper/meta.yml new file mode 100644 index 00000000000..e405e893897 --- /dev/null +++ b/modules/nf-core/pychopper/meta.yml @@ -0,0 +1,54 @@ +name: "pychopper" +description: Identify, orient and trim nanopore cDNA reads +keywords: + - sort + - trimming + - nanopore +tools: + - "pychopper": + description: "A tool to identify, orient and rescue full length cDNA reads from + nanopore data." + homepage: "https://github.com/epi2me-labs/pychopper" + documentation: "https://github.com/epi2me-labs/pychopper" + tool_dev_url: "https://github.com/epi2me-labs/pychopper" + licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"] + identifier: "" + - "gzip": + description: "Gzip reduces the size of the named files using Lempel-Ziv coding + (LZ77)." + documentation: "https://linux.die.net/man/1/gzip" + args_id: "$args3" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: FastQ with reads from long read sequencing e.g. nanopore + pattern: "*.{fastq.gz}" +output: + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{fastq.gz}" + - "*.out.fastq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@chriswyatt1" +maintainers: + - "@chriswyatt1" diff --git a/modules/nf-core/pychopper/tests/main.nf.test b/modules/nf-core/pychopper/tests/main.nf.test new file mode 100644 index 00000000000..c86ec7e942b --- /dev/null +++ b/modules/nf-core/pychopper/tests/main.nf.test @@ -0,0 +1,69 @@ +nextflow_process { + + name "Test Process PYCHOPPER" + script "../main.nf" + process "PYCHOPPER" + tag "pychopper" + tag "modules" + tag "modules_nfcore" + + test("pychopper-test") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id:'test_out' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + + def fastq_content = path(process.out.fastq.get(0).get(1)).linesGzip + + assertAll( + { assert process.success }, + // original pytest checks + { assert process.out.fastq.get(0).get(1) ==~ ".*/test_out.out.fastq.gz" }, + // additional nf-test checks + // Order of reads is not deterministic, so only assess whether the number of reads is correct + { assert snapshot( + process.out.fastq, + process.out.versions + ).match() } + ) + } + } + + test("test-pychopper-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [id:'test_out' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fastq, + process.out.versions + ).match() } + ) + } + } + +} diff --git a/modules/nf-core/pychopper/tests/main.nf.test.snap b/modules/nf-core/pychopper/tests/main.nf.test.snap new file mode 100644 index 00000000000..c94ecdba34e --- /dev/null +++ b/modules/nf-core/pychopper/tests/main.nf.test.snap @@ -0,0 +1,42 @@ +{ + "pychopper-test": { + "content": [ + [ + [ + { + "id": "test_out" + }, + "test_out.out.fastq.gz:md5,04f3003f5cb5a78d90cae351beacb094" + ] + ], + [ + "versions.yml:md5,1431ed95e3c77f8742c7b014b26e50f5" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-05T13:57:08.581810556" + }, + "test-pychopper-stub": { + "content": [ + [ + [ + { + "id": "test_out" + }, + "test_out.out.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,1431ed95e3c77f8742c7b014b26e50f5" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-05T15:09:38.47491875" + } +} \ No newline at end of file diff --git a/modules/nf-core/pycoqc/environment.yml b/modules/nf-core/pycoqc/environment.yml index 6c0c93e98c0..8637d0435c7 100644 --- a/modules/nf-core/pycoqc/environment.yml +++ b/modules/nf-core/pycoqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pydamage/analyze/environment.yml b/modules/nf-core/pydamage/analyze/environment.yml index f1193aab4ea..dc4ff1fa455 100644 --- a/modules/nf-core/pydamage/analyze/environment.yml +++ b/modules/nf-core/pydamage/analyze/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pydamage/filter/environment.yml b/modules/nf-core/pydamage/filter/environment.yml index f1193aab4ea..dc4ff1fa455 100644 --- a/modules/nf-core/pydamage/filter/environment.yml +++ b/modules/nf-core/pydamage/filter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml b/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml index d18360bed97..36c4150bd25 100644 --- a/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml +++ b/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pypgx=0.25.0" + - bioconda::pypgx=0.25.0 diff --git a/modules/nf-core/qcat/environment.yml b/modules/nf-core/qcat/environment.yml index 0ab0d71b8f8..f046577c4a2 100644 --- a/modules/nf-core/qcat/environment.yml +++ b/modules/nf-core/qcat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/qualimap/bamqc/environment.yml b/modules/nf-core/qualimap/bamqc/environment.yml index 4fa5f4e8e9d..4574291d34f 100644 --- a/modules/nf-core/qualimap/bamqc/environment.yml +++ b/modules/nf-core/qualimap/bamqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/qualimap/bamqccram/environment.yml b/modules/nf-core/qualimap/bamqccram/environment.yml index 609b5f74a80..8ea03600f13 100644 --- a/modules/nf-core/qualimap/bamqccram/environment.yml +++ b/modules/nf-core/qualimap/bamqccram/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 4fa5f4e8e9d..4574291d34f 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/quartonotebook/environment.yml b/modules/nf-core/quartonotebook/environment.yml index b79fb2e075e..037c6f676e6 100644 --- a/modules/nf-core/quartonotebook/environment.yml +++ b/modules/nf-core/quartonotebook/environment.yml @@ -1,15 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: # renovate: datasource=conda depName=conda-forge/quarto # FIXME https://github.com/nf-core/modules/issues/7006 - - conda-forge::quarto=1.5.57 - # renovate: datasource=conda depName=conda-forge/jupyter - conda-forge::jupyter=1.0.0 - # renovate: datasource=conda depName=conda-forge/matplotlib - conda-forge::matplotlib=3.4.3 - # renovate: datasource=conda depName=conda-forge/papermill - conda-forge::papermill=2.4.0 - # renovate: datasource=conda depName=conda-forge/r-rmarkdown + - conda-forge::quarto=1.5.57 - conda-forge::r-rmarkdown=2.25 diff --git a/modules/nf-core/quast/environment.yml b/modules/nf-core/quast/environment.yml index 2c14403de7a..c571a75fcb4 100644 --- a/modules/nf-core/quast/environment.yml +++ b/modules/nf-core/quast/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/quilt/quilt/environment.yml b/modules/nf-core/quilt/quilt/environment.yml index 967b84ba314..2ed39624b80 100644 --- a/modules/nf-core/quilt/quilt/environment.yml +++ b/modules/nf-core/quilt/quilt/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/racon/environment.yml b/modules/nf-core/racon/environment.yml index b210a3db8fa..bd714ce3720 100644 --- a/modules/nf-core/racon/environment.yml +++ b/modules/nf-core/racon/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rapidnj/environment.yml b/modules/nf-core/rapidnj/environment.yml index d18144a400a..99efa3d8aa4 100644 --- a/modules/nf-core/rapidnj/environment.yml +++ b/modules/nf-core/rapidnj/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rasusa/environment.yml b/modules/nf-core/rasusa/environment.yml index e2e81834b6d..68cd6e403fe 100644 --- a/modules/nf-core/rasusa/environment.yml +++ b/modules/nf-core/rasusa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/raven/environment.yml b/modules/nf-core/raven/environment.yml index c520dacbfb2..c124c2c5e33 100644 --- a/modules/nf-core/raven/environment.yml +++ b/modules/nf-core/raven/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/raxmlng/environment.yml b/modules/nf-core/raxmlng/environment.yml index 28e81c36a38..6d1b3cf0c02 100644 --- a/modules/nf-core/raxmlng/environment.yml +++ b/modules/nf-core/raxmlng/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/regtools/junctionsextract/environment.yml b/modules/nf-core/regtools/junctionsextract/environment.yml index 2b615890f84..29ee2ee71b0 100644 --- a/modules/nf-core/regtools/junctionsextract/environment.yml +++ b/modules/nf-core/regtools/junctionsextract/environment.yml @@ -1,6 +1,7 @@ +--- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::regtools=1.0.0" + - bioconda::regtools=1.0.0 diff --git a/modules/nf-core/repeatmodeler/builddatabase/environment.yml b/modules/nf-core/repeatmodeler/builddatabase/environment.yml index 531430738c6..3f04be8dff4 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/environment.yml +++ b/modules/nf-core/repeatmodeler/builddatabase/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::repeatmodeler=2.0.5" + - bioconda::repeatmodeler=2.0.5 diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml index 531430738c6..3f04be8dff4 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml +++ b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::repeatmodeler=2.0.5" + - bioconda::repeatmodeler=2.0.5 diff --git a/modules/nf-core/resfinder/run/environment.yml b/modules/nf-core/resfinder/run/environment.yml index 823ba211777..207ed5642ad 100644 --- a/modules/nf-core/resfinder/run/environment.yml +++ b/modules/nf-core/resfinder/run/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::resfinder=4.1.11" + - bioconda::resfinder=4.1.11 diff --git a/modules/nf-core/rgi/cardannotation/environment.yml b/modules/nf-core/rgi/cardannotation/environment.yml index 609693fe947..a316932453d 100644 --- a/modules/nf-core/rgi/cardannotation/environment.yml +++ b/modules/nf-core/rgi/cardannotation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rgi/main/environment.yml b/modules/nf-core/rgi/main/environment.yml index 609693fe947..a316932453d 100644 --- a/modules/nf-core/rgi/main/environment.yml +++ b/modules/nf-core/rgi/main/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rhocall/annotate/environment.yml b/modules/nf-core/rhocall/annotate/environment.yml index ba95c3cbeb1..8a0fe435e74 100644 --- a/modules/nf-core/rhocall/annotate/environment.yml +++ b/modules/nf-core/rhocall/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rhocall/viz/environment.yml b/modules/nf-core/rhocall/viz/environment.yml index 538db5092da..8a0fe435e74 100644 --- a/modules/nf-core/rhocall/viz/environment.yml +++ b/modules/nf-core/rhocall/viz/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::rhocall=0.5.1" + - bioconda::rhocall=0.5.1 diff --git a/modules/nf-core/ribotish/predict/environment.yml b/modules/nf-core/ribotish/predict/environment.yml index c96eb9589db..65bb256c539 100644 --- a/modules/nf-core/ribotish/predict/environment.yml +++ b/modules/nf-core/ribotish/predict/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ribotish=0.2.7" + - bioconda::ribotish=0.2.7 diff --git a/modules/nf-core/ribotish/quality/environment.yml b/modules/nf-core/ribotish/quality/environment.yml index c96eb9589db..65bb256c539 100644 --- a/modules/nf-core/ribotish/quality/environment.yml +++ b/modules/nf-core/ribotish/quality/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ribotish=0.2.7" + - bioconda::ribotish=0.2.7 diff --git a/modules/nf-core/ribotricer/detectorfs/environment.yml b/modules/nf-core/ribotricer/detectorfs/environment.yml index 3284c86d00b..d94928654c7 100644 --- a/modules/nf-core/ribotricer/detectorfs/environment.yml +++ b/modules/nf-core/ribotricer/detectorfs/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ribotricer=1.3.3" + - bioconda::ribotricer=1.3.3 diff --git a/modules/nf-core/ribotricer/prepareorfs/environment.yml b/modules/nf-core/ribotricer/prepareorfs/environment.yml index 3284c86d00b..d94928654c7 100644 --- a/modules/nf-core/ribotricer/prepareorfs/environment.yml +++ b/modules/nf-core/ribotricer/prepareorfs/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ribotricer=1.3.3" + - bioconda::ribotricer=1.3.3 diff --git a/modules/nf-core/ribowaltz/environment.yml b/modules/nf-core/ribowaltz/environment.yml index 8cc74d39146..55f914221f0 100644 --- a/modules/nf-core/ribowaltz/environment.yml +++ b/modules/nf-core/ribowaltz/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ribowaltz=2.0" + - bioconda::ribowaltz=2.0 diff --git a/modules/nf-core/ripgrep/environment.yml b/modules/nf-core/ripgrep/environment.yml index af129f6b150..ffe1c14f4ea 100644 --- a/modules/nf-core/ripgrep/environment.yml +++ b/modules/nf-core/ripgrep/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rmarkdownnotebook/environment.yml b/modules/nf-core/rmarkdownnotebook/environment.yml index 26cd9e2e138..21fc637f7a8 100644 --- a/modules/nf-core/rmarkdownnotebook/environment.yml +++ b/modules/nf-core/rmarkdownnotebook/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/roary/environment.yml b/modules/nf-core/roary/environment.yml index 87b7f3906dc..1ee55e664c8 100644 --- a/modules/nf-core/roary/environment.yml +++ b/modules/nf-core/roary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index bcf70fa9adf..4b358a32b6b 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index bcf70fa9adf..4b358a32b6b 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 304e38fcfd0..f1dc909fc5e 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rtgtools/format/environment.yml b/modules/nf-core/rtgtools/format/environment.yml index 8aa83cdc41d..f142abd3819 100644 --- a/modules/nf-core/rtgtools/format/environment.yml +++ b/modules/nf-core/rtgtools/format/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rtgtools/pedfilter/environment.yml b/modules/nf-core/rtgtools/pedfilter/environment.yml index 8aa83cdc41d..f142abd3819 100644 --- a/modules/nf-core/rtgtools/pedfilter/environment.yml +++ b/modules/nf-core/rtgtools/pedfilter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rtgtools/rocplot/environment.yml b/modules/nf-core/rtgtools/rocplot/environment.yml index 8aa83cdc41d..f142abd3819 100644 --- a/modules/nf-core/rtgtools/rocplot/environment.yml +++ b/modules/nf-core/rtgtools/rocplot/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index 8aa83cdc41d..f142abd3819 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sageproteomics/sage/environment.yml b/modules/nf-core/sageproteomics/sage/environment.yml index 8fdc7c73fbc..29b6cda91d4 100644 --- a/modules/nf-core/sageproteomics/sage/environment.yml +++ b/modules/nf-core/sageproteomics/sage/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sage-proteomics=0.14.7" + - bioconda::sage-proteomics=0.14.7 diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index b3f75777e46..c9d53143499 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index b3f75777e46..c9d53143499 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/salsa2/environment.yml b/modules/nf-core/salsa2/environment.yml index 8684652eee3..867c3086d23 100644 --- a/modules/nf-core/salsa2/environment.yml +++ b/modules/nf-core/salsa2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sam2lca/analyze/environment.yml b/modules/nf-core/sam2lca/analyze/environment.yml index 7d8bbaa297e..af73164c8ea 100644 --- a/modules/nf-core/sam2lca/analyze/environment.yml +++ b/modules/nf-core/sam2lca/analyze/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sambamba/flagstat/environment.yml b/modules/nf-core/sambamba/flagstat/environment.yml index cebae1edf70..a2609235138 100644 --- a/modules/nf-core/sambamba/flagstat/environment.yml +++ b/modules/nf-core/sambamba/flagstat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sambamba/markdup/environment.yml b/modules/nf-core/sambamba/markdup/environment.yml index cebae1edf70..a2609235138 100644 --- a/modules/nf-core/sambamba/markdup/environment.yml +++ b/modules/nf-core/sambamba/markdup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml index fc8cd9e5158..a24590a5e9f 100644 --- a/modules/nf-core/samblaster/environment.yml +++ b/modules/nf-core/samblaster/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/samshee/environment.yml b/modules/nf-core/samshee/environment.yml index 09203856bfe..20bf67d53b9 100644 --- a/modules/nf-core/samshee/environment.yml +++ b/modules/nf-core/samshee/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/sormadup/main.nf b/modules/nf-core/samtools/sormadup/main.nf index e8ac9b1c7ee..b20d69f0d35 100644 --- a/modules/nf-core/samtools/sormadup/main.nf +++ b/modules/nf-core/samtools/sormadup/main.nf @@ -33,7 +33,9 @@ process SAMTOOLS_SORMADUP { args5.contains("--output-fmt cram") ? "cram" : "bam" def reference = fasta ? "--reference ${fasta}" : "" - def sort_memory = (task.memory.mega/task.cpus*0.75).intValue() + // memory per thread for samtools sort + // set to 50% of the memory per thread, but at least 768M (samtools default) + def sort_memory = Math.max(768,(task.memory.mega/task.cpus*0.50).intValue()) """ samtools cat \\ @@ -69,6 +71,7 @@ process SAMTOOLS_SORMADUP { -T ${prefix} \\ -f ${prefix}.metrics \\ --threads $task.cpus \\ + $reference \\ $args5 \\ - \\ ${prefix}.${extension} diff --git a/modules/nf-core/samtools/sormadup/tests/bam.config b/modules/nf-core/samtools/sormadup/tests/bam.config new file mode 100644 index 00000000000..9ef2071a158 --- /dev/null +++ b/modules/nf-core/samtools/sormadup/tests/bam.config @@ -0,0 +1,12 @@ +process { + withName: "SAMTOOLS_SORMADUP" { + ext.prefix = {"${meta.id}.merged"} + ext.args5 = {[ + "-s", // print some stats + "--json", // output stats in json format for MultiQC + "-d 2500", // The optical duplicate distance + "--barcode-name", // Use the UMI/barcode embedded in the read name (eigth colon delimited part). + "--write-index", // Write csi/crai index + ].join(" ").trim()} + } +} diff --git a/modules/nf-core/samtools/sormadup/tests/cram.config b/modules/nf-core/samtools/sormadup/tests/cram.config new file mode 100644 index 00000000000..8d6ce11a2d5 --- /dev/null +++ b/modules/nf-core/samtools/sormadup/tests/cram.config @@ -0,0 +1,14 @@ +process { + withName: "SAMTOOLS_SORMADUP" { + ext.prefix = {"${meta.id}.merged"} + ext.args5 = {[ + "-s", // print some stats + "--json", // output stats in json format for MultiQC + "-d 2500", // The optical duplicate distance + "--barcode-name", // Use the UMI/barcode embedded in the read name (eigth colon delimited part). + "--write-index", // Write csi/crai index + "--output-fmt cram", // Output format + "--output-fmt-option archive" // Cram compression level + ].join(" ").trim()} + } +} diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test b/modules/nf-core/samtools/sormadup/tests/main.nf.test index 031b022f88f..574d70c6afc 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test @@ -34,6 +34,46 @@ nextflow_process { } } + test("sarscov2 - cram") { + config "./cram.config" + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + } + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + def fasta = params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta' + assertAll( + { assert process.success }, + { + assert snapshot( + cram( + process.out.cram[0][1], + fasta, + ).getReadsMD5(), + file(process.out.crai[0][1]).name, + process.out.metrics, + ).match() + } + ) + } + } + + test("sarscov2 - bam - stub") { options "-stub" diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap index 0a38f7f0c37..567766053f4 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap @@ -70,6 +70,26 @@ }, "timestamp": "2024-09-16T08:56:24.200237922" }, + "sarscov2 - cram": { + "content": [ + "5a5baeea55f04def40fd3070318e5a3", + "test.merged.cram.crai", + [ + [ + { + "id": "test", + "single_end": false + }, + "test.merged.metrics:md5,548ff6d0d22ef710858639fe22e90004" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-05T12:24:12.517796" + }, "sarscov2 - bam": { "content": [ { @@ -79,7 +99,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" + "test.bam:md5,4dd85f1abbd2806887c6942f9c84595a" ] ], "1": [ @@ -97,7 +117,7 @@ "id": "test", "single_end": false }, - "test.metrics:md5,bed5fec5c6c55500f10042eba21f9d13" + "test.metrics:md5,6093d8853805578a1868f22ff68177e7" ] ], "5": [ @@ -109,7 +129,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" + "test.bam:md5,4dd85f1abbd2806887c6942f9c84595a" ] ], "crai": [ @@ -127,7 +147,7 @@ "id": "test", "single_end": false }, - "test.metrics:md5,bed5fec5c6c55500f10042eba21f9d13" + "test.metrics:md5,6093d8853805578a1868f22ff68177e7" ] ], "versions": [ @@ -136,9 +156,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-09-16T08:56:12.101922642" + "timestamp": "2025-02-05T11:48:51.866973" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 02cda6e6a3b..8cae5712d5e 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -6,5 +6,4 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/htslib - bioconda::htslib=1.21 - # renovate: datasource=conda depName=bioconda/samtools - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index a6941e63888..4f69a94bc45 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data' : - 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/scds/environment.yml b/modules/nf-core/scds/environment.yml index c438cee51fd..cddd5ade72e 100644 --- a/modules/nf-core/scds/environment.yml +++ b/modules/nf-core/scds/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/scoary/environment.yml b/modules/nf-core/scoary/environment.yml index 6ee2f49249e..d339cbf650c 100644 --- a/modules/nf-core/scoary/environment.yml +++ b/modules/nf-core/scoary/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/scramble/clusteranalysis/environment.yml b/modules/nf-core/scramble/clusteranalysis/environment.yml index f0eecd4590f..ac5eae73c03 100644 --- a/modules/nf-core/scramble/clusteranalysis/environment.yml +++ b/modules/nf-core/scramble/clusteranalysis/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/scramble/clusteridentifier/environment.yml b/modules/nf-core/scramble/clusteridentifier/environment.yml index f0eecd4590f..ac5eae73c03 100644 --- a/modules/nf-core/scramble/clusteridentifier/environment.yml +++ b/modules/nf-core/scramble/clusteridentifier/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/scvitools/scar/environment.yml b/modules/nf-core/scvitools/scar/environment.yml index c0df8f5baca..6464e9e2bc8 100644 --- a/modules/nf-core/scvitools/scar/environment.yml +++ b/modules/nf-core/scvitools/scar/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/scvitools/solo/environment.yml b/modules/nf-core/scvitools/solo/environment.yml index b5a28d3c2f8..30051a3e61a 100644 --- a/modules/nf-core/scvitools/solo/environment.yml +++ b/modules/nf-core/scvitools/solo/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seacr/callpeak/environment.yml b/modules/nf-core/seacr/callpeak/environment.yml index 4fac3de656e..9103ff31dfa 100644 --- a/modules/nf-core/seacr/callpeak/environment.yml +++ b/modules/nf-core/seacr/callpeak/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/segemehl/align/environment.yml b/modules/nf-core/segemehl/align/environment.yml index e37058da852..9efa92cb8b3 100644 --- a/modules/nf-core/segemehl/align/environment.yml +++ b/modules/nf-core/segemehl/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/segemehl/index/environment.yml b/modules/nf-core/segemehl/index/environment.yml index e37058da852..9efa92cb8b3 100644 --- a/modules/nf-core/segemehl/index/environment.yml +++ b/modules/nf-core/segemehl/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/semibin/singleeasybin/environment.yml b/modules/nf-core/semibin/singleeasybin/environment.yml index 5830810b1f4..a4d17e4350d 100644 --- a/modules/nf-core/semibin/singleeasybin/environment.yml +++ b/modules/nf-core/semibin/singleeasybin/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/applyvarcal/environment.yml +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/bwaindex/environment.yml b/modules/nf-core/sentieon/bwaindex/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/bwaindex/environment.yml +++ b/modules/nf-core/sentieon/bwaindex/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/collectvcmetrics/environment.yml b/modules/nf-core/sentieon/collectvcmetrics/environment.yml index d1a652d9586..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/environment.yml +++ b/modules/nf-core/sentieon/collectvcmetrics/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sentieon=202308.03" + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/coveragemetrics/environment.yml b/modules/nf-core/sentieon/coveragemetrics/environment.yml index d1a652d9586..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/coveragemetrics/environment.yml +++ b/modules/nf-core/sentieon/coveragemetrics/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sentieon=202308.03" + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/datametrics/environment.yml b/modules/nf-core/sentieon/datametrics/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/datametrics/environment.yml +++ b/modules/nf-core/sentieon/datametrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/gvcftyper/environment.yml +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/haplotyper/environment.yml +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/qualcal/environment.yml b/modules/nf-core/sentieon/qualcal/environment.yml index d1a652d9586..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/qualcal/environment.yml +++ b/modules/nf-core/sentieon/qualcal/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sentieon=202308.03" + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/readwriter/environment.yml b/modules/nf-core/sentieon/readwriter/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/readwriter/environment.yml +++ b/modules/nf-core/sentieon/readwriter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/tnfilter/environment.yml b/modules/nf-core/sentieon/tnfilter/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/tnfilter/environment.yml +++ b/modules/nf-core/sentieon/tnfilter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml +++ b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/tnscope/environment.yml b/modules/nf-core/sentieon/tnscope/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/tnscope/environment.yml +++ b/modules/nf-core/sentieon/tnscope/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/varcal/environment.yml +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sentieon/wgsmetrics/environment.yml b/modules/nf-core/sentieon/wgsmetrics/environment.yml index d7abf668ea9..6449d0dbb9a 100644 --- a/modules/nf-core/sentieon/wgsmetrics/environment.yml +++ b/modules/nf-core/sentieon/wgsmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqcluster/collapse/environment.yml b/modules/nf-core/seqcluster/collapse/environment.yml index 1263856a43e..f8909bf89b9 100644 --- a/modules/nf-core/seqcluster/collapse/environment.yml +++ b/modules/nf-core/seqcluster/collapse/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::seqcluster=1.2.9" + - bioconda::seqcluster=1.2.9 diff --git a/modules/nf-core/seqfu/derep/environment.yml b/modules/nf-core/seqfu/derep/environment.yml index 8fa07dfce05..d7a9c630915 100644 --- a/modules/nf-core/seqfu/derep/environment.yml +++ b/modules/nf-core/seqfu/derep/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqfu=1.20.3" + - bioconda::seqfu=1.20.3 diff --git a/modules/nf-core/seqfu/stats/environment.yml b/modules/nf-core/seqfu/stats/environment.yml index 8fa07dfce05..d7a9c630915 100644 --- a/modules/nf-core/seqfu/stats/environment.yml +++ b/modules/nf-core/seqfu/stats/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqfu=1.20.3" + - bioconda::seqfu=1.20.3 diff --git a/modules/nf-core/seqkit/concat/environment.yml b/modules/nf-core/seqkit/concat/environment.yml index 160a67c08e8..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/concat/environment.yml +++ b/modules/nf-core/seqkit/concat/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqkit=2.9.0" + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/fq2fa/environment.yml b/modules/nf-core/seqkit/fq2fa/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/fq2fa/environment.yml +++ b/modules/nf-core/seqkit/fq2fa/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/fx2tab/environment.yml b/modules/nf-core/seqkit/fx2tab/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/fx2tab/environment.yml +++ b/modules/nf-core/seqkit/fx2tab/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/grep/environment.yml b/modules/nf-core/seqkit/grep/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/grep/environment.yml +++ b/modules/nf-core/seqkit/grep/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/pair/environment.yml b/modules/nf-core/seqkit/pair/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/pair/environment.yml +++ b/modules/nf-core/seqkit/pair/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/replace/environment.yml +++ b/modules/nf-core/seqkit/replace/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/rmdup/environment.yml b/modules/nf-core/seqkit/rmdup/environment.yml index 160a67c08e8..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/rmdup/environment.yml +++ b/modules/nf-core/seqkit/rmdup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqkit=2.9.0" + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/seq/environment.yml b/modules/nf-core/seqkit/seq/environment.yml index 160a67c08e8..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/seq/environment.yml +++ b/modules/nf-core/seqkit/seq/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqkit=2.9.0" + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/sliding/environment.yml b/modules/nf-core/seqkit/sliding/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/sliding/environment.yml +++ b/modules/nf-core/seqkit/sliding/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/sort/environment.yml b/modules/nf-core/seqkit/sort/environment.yml index 160a67c08e8..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/sort/environment.yml +++ b/modules/nf-core/seqkit/sort/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqkit=2.9.0" + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqkit/split2/environment.yml b/modules/nf-core/seqkit/split2/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/split2/environment.yml +++ b/modules/nf-core/seqkit/split2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/stats/environment.yml b/modules/nf-core/seqkit/stats/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/stats/environment.yml +++ b/modules/nf-core/seqkit/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/tab2fx/environment.yml b/modules/nf-core/seqkit/tab2fx/environment.yml index 1f93892f485..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/tab2fx/environment.yml +++ b/modules/nf-core/seqkit/tab2fx/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqkit/translate/environment.yml b/modules/nf-core/seqkit/translate/environment.yml index f917ae67580..b26fb1eb8c5 100644 --- a/modules/nf-core/seqkit/translate/environment.yml +++ b/modules/nf-core/seqkit/translate/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::seqkit=2.9.0" + - bioconda::seqkit=2.9.0 diff --git a/modules/nf-core/seqsero2/environment.yml b/modules/nf-core/seqsero2/environment.yml index b312bdd67b6..84348ddffa4 100644 --- a/modules/nf-core/seqsero2/environment.yml +++ b/modules/nf-core/seqsero2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/cutn/environment.yml b/modules/nf-core/seqtk/cutn/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/cutn/environment.yml +++ b/modules/nf-core/seqtk/cutn/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/mergepe/environment.yml b/modules/nf-core/seqtk/mergepe/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/mergepe/environment.yml +++ b/modules/nf-core/seqtk/mergepe/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/rename/environment.yml b/modules/nf-core/seqtk/rename/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/rename/environment.yml +++ b/modules/nf-core/seqtk/rename/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/sample/environment.yml +++ b/modules/nf-core/seqtk/sample/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/seq/environment.yml b/modules/nf-core/seqtk/seq/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/seq/environment.yml +++ b/modules/nf-core/seqtk/seq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/subseq/environment.yml b/modules/nf-core/seqtk/subseq/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/subseq/environment.yml +++ b/modules/nf-core/seqtk/subseq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/trim/environment.yml b/modules/nf-core/seqtk/trim/environment.yml index 693aa5c1770..b1d11cbd2ae 100644 --- a/modules/nf-core/seqtk/trim/environment.yml +++ b/modules/nf-core/seqtk/trim/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sequencetools/pileupcaller/environment.yml b/modules/nf-core/sequencetools/pileupcaller/environment.yml index 487e2fcd728..2c5ad3ba1c9 100644 --- a/modules/nf-core/sequencetools/pileupcaller/environment.yml +++ b/modules/nf-core/sequencetools/pileupcaller/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sequenzautils/bam2seqz/environment.yml b/modules/nf-core/sequenzautils/bam2seqz/environment.yml index b98667bf063..4a93a61b4c6 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/environment.yml +++ b/modules/nf-core/sequenzautils/bam2seqz/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sequenzautils/gcwiggle/environment.yml b/modules/nf-core/sequenzautils/gcwiggle/environment.yml index 6713252e2d9..3ceec10008f 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/environment.yml +++ b/modules/nf-core/sequenzautils/gcwiggle/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqwish/induce/environment.yml b/modules/nf-core/seqwish/induce/environment.yml index eca0130c973..b9d0a1e1fd0 100644 --- a/modules/nf-core/seqwish/induce/environment.yml +++ b/modules/nf-core/seqwish/induce/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seroba/run/environment.yml b/modules/nf-core/seroba/run/environment.yml index 470f7538175..49467946a99 100644 --- a/modules/nf-core/seroba/run/environment.yml +++ b/modules/nf-core/seroba/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/severus/environment.yml b/modules/nf-core/severus/environment.yml index 17775d4fcbe..6081c124e86 100644 --- a/modules/nf-core/severus/environment.yml +++ b/modules/nf-core/severus/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::severus=1.3" + - bioconda::severus=1.3 diff --git a/modules/nf-core/sexdeterrmine/environment.yml b/modules/nf-core/sexdeterrmine/environment.yml index 62fc8995223..4117cfb68e9 100644 --- a/modules/nf-core/sexdeterrmine/environment.yml +++ b/modules/nf-core/sexdeterrmine/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sgdemux/environment.yml b/modules/nf-core/sgdemux/environment.yml index ce09711afd0..5215292ad4f 100644 --- a/modules/nf-core/sgdemux/environment.yml +++ b/modules/nf-core/sgdemux/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shapeit5/ligate/environment.yml b/modules/nf-core/shapeit5/ligate/environment.yml index 91b87fd02eb..8080aee1ca4 100644 --- a/modules/nf-core/shapeit5/ligate/environment.yml +++ b/modules/nf-core/shapeit5/ligate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shapeit5/phasecommon/environment.yml b/modules/nf-core/shapeit5/phasecommon/environment.yml index 91b87fd02eb..8080aee1ca4 100644 --- a/modules/nf-core/shapeit5/phasecommon/environment.yml +++ b/modules/nf-core/shapeit5/phasecommon/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shapeit5/phaserare/environment.yml b/modules/nf-core/shapeit5/phaserare/environment.yml index 91b87fd02eb..8080aee1ca4 100644 --- a/modules/nf-core/shapeit5/phaserare/environment.yml +++ b/modules/nf-core/shapeit5/phaserare/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shapeit5/switch/environment.yml b/modules/nf-core/shapeit5/switch/environment.yml index 91b87fd02eb..8080aee1ca4 100644 --- a/modules/nf-core/shapeit5/switch/environment.yml +++ b/modules/nf-core/shapeit5/switch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shasta/environment.yml b/modules/nf-core/shasta/environment.yml index 6b8d44850ec..ebfde21625b 100644 --- a/modules/nf-core/shasta/environment.yml +++ b/modules/nf-core/shasta/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shasum/environment.yml b/modules/nf-core/shasum/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/shasum/environment.yml +++ b/modules/nf-core/shasum/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shigatyper/environment.yml b/modules/nf-core/shigatyper/environment.yml index e48e73b7ae7..9ad40da1df4 100644 --- a/modules/nf-core/shigatyper/environment.yml +++ b/modules/nf-core/shigatyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shigeifinder/environment.yml b/modules/nf-core/shigeifinder/environment.yml index 8ea18f13b52..778691f653a 100644 --- a/modules/nf-core/shigeifinder/environment.yml +++ b/modules/nf-core/shigeifinder/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml index f98b8bf5493..9e88075c5f0 100644 --- a/modules/nf-core/shinyngs/app/environment.yml +++ b/modules/nf-core/shinyngs/app/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml index f98b8bf5493..9e88075c5f0 100644 --- a/modules/nf-core/shinyngs/staticdifferential/environment.yml +++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml index f98b8bf5493..9e88075c5f0 100644 --- a/modules/nf-core/shinyngs/staticexploratory/environment.yml +++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml index f98b8bf5493..9e88075c5f0 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/shovill/environment.yml b/modules/nf-core/shovill/environment.yml index 4f351ad0052..47fd1dd04a7 100644 --- a/modules/nf-core/shovill/environment.yml +++ b/modules/nf-core/shovill/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sickle/environment.yml b/modules/nf-core/sickle/environment.yml index d03c86e18e3..cd664ed21a5 100644 --- a/modules/nf-core/sickle/environment.yml +++ b/modules/nf-core/sickle/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/simpleaf/index/environment.yml b/modules/nf-core/simpleaf/index/environment.yml index 7e7a1020431..9053723238e 100644 --- a/modules/nf-core/simpleaf/index/environment.yml +++ b/modules/nf-core/simpleaf/index/environment.yml @@ -1,9 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - bioconda - conda-forge dependencies: - bioconda::alevin-fry=0.11.1 - - bioconda::piscem=0.11.0 + - bioconda::piscem=0.12.2 - bioconda::salmon=1.10.3 - - bioconda::simpleaf=0.18.4 + - bioconda::simpleaf=0.19.1 diff --git a/modules/nf-core/simpleaf/index/main.nf b/modules/nf-core/simpleaf/index/main.nf index 5959c7ddbcb..d251f6a1ce0 100644 --- a/modules/nf-core/simpleaf/index/main.nf +++ b/modules/nf-core/simpleaf/index/main.nf @@ -5,12 +5,14 @@ process SIMPLEAF_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/simpleaf:0.18.4--ha6fb395_1': - 'biocontainers/simpleaf:0.18.4--ha6fb395_1' }" + 'https://depot.galaxyproject.org/singularity/simpleaf:0.19.1--ha6fb395_0': + 'biocontainers/simpleaf:0.19.1--ha6fb395_0' }" input: tuple val(meta), path(genome_fasta), path(genome_gtf) tuple val(meta2), path(transcript_fasta) + tuple val(meta3), path(probe_csv) + tuple val(meta4), path(feature_csv) output: tuple val(meta), path("${prefix}/index") , emit: index @@ -23,10 +25,9 @@ process SIMPLEAF_INDEX { script: def args = task.ext.args ?: '' - def seq_inputs = input_args(genome_fasta, genome_gtf, transcript_fasta)//, probes_csv, features_csv) + (meta, seq_inputs) = input_args(genome_fasta, genome_gtf, transcript_fasta, probe_csv, feature_csv, meta, meta2, meta3, meta4) // Output meta needs to correspond to the input used - meta = (transcript_fasta) ? meta2 : meta prefix = task.ext.prefix ?: "${meta.id}" """ # export required var @@ -56,8 +57,8 @@ process SIMPLEAF_INDEX { """ stub: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : "${meta2.id}") + meta = meta ? meta : [id: 'stub'] + prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}/index @@ -78,19 +79,22 @@ process SIMPLEAF_INDEX { """ } -def input_args(genome_fasta, genome_gtf, transcript_fasta) { //, probes_csv, features_csv) { - // if (probe_csv) { - // args = "--probe_csv ${probe_csv}" - // } else if (feature_csv) { - // args = "--feature_csv ${feature_csv}" - // } else - if (transcript_fasta) { - return "--ref-seq ${transcript_fasta}" +def input_args(genome_fasta, genome_gtf, transcript_fasta, probe_csv, feature_csv, meta, meta2, meta3, meta4) { + // check if all null + if (!genome_fasta && !genome_gtf && !transcript_fasta && !probe_csv && !feature_csv) { + error "No valid input provided; please provide either a genome fasta + gtf set or a transcript fasta file." + } + + if (feature_csv) { + return [meta4, "--feature-csv ${feature_csv}"] + } else if (probe_csv) { + return [meta3, "--probe-csv ${probe_csv}"] + } else if (transcript_fasta) { + return [meta2, "--ref-seq ${transcript_fasta}"] } else if (genome_fasta && genome_gtf) { - return "--fasta ${genome_fasta} --gtf ${genome_gtf}" + return [meta, "--fasta ${genome_fasta} --gtf ${genome_gtf}"] } else { - error "No valid input provided; please provide either a genome fasta + gtf set or a transcript fasta file. ${genome_fasta} ${genome_gtf} ${transcript_fasta}" - // error "No valid input provided; please provide one of the followings: (i) a genome fasta + gtf set, (ii) a transcript fasta file, (iii) a probes csv file (iv) a features csv file." + error "No valid input provided; please provide one of the followings: (i) a genome fasta + gtf set, (ii) a transcript fasta file, (iii) a probes csv file (iv) a features csv file." } } diff --git a/modules/nf-core/simpleaf/index/meta.yml b/modules/nf-core/simpleaf/index/meta.yml index a9c5e66b90c..b13c591b552 100644 --- a/modules/nf-core/simpleaf/index/meta.yml +++ b/modules/nf-core/simpleaf/index/meta.yml @@ -20,17 +20,13 @@ input: - genome_fasta: type: file description: | - FASTA file containing the genome sequence. - It conflicts with transcript_fasta. - When transcript_fasta is provided, it must be empty (provided as []). - When transcript_fasta is empty, it must be provided together with its corresponding genome_gtf file. + FASTA file containing the genome sequence. It must be provided together with the corresponding genome_gtf file. + When another input set is provided, it must be empty (provided as []). - genome_gtf: type: file description: | - GTF file containing gene annotations. - It conflicts with transcript_fasta. - When transcript_fasta is provided, it must be empty (provided as []). - When transcript_fasta is empty, it must be provided together with its corresponding genome_fasta file. + GTF file containing gene annotations. It must be provided together with its corresponding genome_fasta file. + When another input set rather than genome_fasta + genome_gtf is provided, it must be empty (provided as []). - - meta2: type: map description: | @@ -39,8 +35,25 @@ input: type: file description: | FASTA file containing the transcript sequences to build index directly on. - It conflicts with genome_gtf and genome_fasta. - When genome_gtf and genome_fasta are provided, it must be empty (provided as []). + When another input set is provided, it must be empty (provided as []). + - - meta3: + type: map + description: | + Groovy Map containing information on probe_csv. + - probe_csv: + type: file + description: | + CSV file containing the reference probe sequences to build index directly on. + When another input set is provided, it must be empty (provided as []). + - - meta4: + type: map + description: | + Groovy Map containing information on feature_csv. + - feature_csv: + type: file + description: | + CSV file containing the reference feature barcodes to build index directly on. + When another input set is provided, it must be empty (provided as []). output: - index: - meta: diff --git a/modules/nf-core/simpleaf/index/tests/main.nf.test b/modules/nf-core/simpleaf/index/tests/main.nf.test index d546967d62e..3f76e238038 100644 --- a/modules/nf-core/simpleaf/index/tests/main.nf.test +++ b/modules/nf-core/simpleaf/index/tests/main.nf.test @@ -21,6 +21,8 @@ nextflow_process { input[0] = Channel.of([ meta, genome_fasta, gtf ]) input[1] = Channel.of([[],[]]) + input[2] = Channel.of([[],[]]) + input[3] = Channel.of([[],[]]) """ } } @@ -56,6 +58,80 @@ nextflow_process { input[0] = Channel.of([[],[],[]]) input[1] = Channel.of([ meta, transcriptome_fasta ]) + input[2] = Channel.of([[],[]]) + input[3] = Channel.of([[],[]]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx_cfish.json").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.ctab").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.ectab").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.json").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.refinfo").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.sshash").exists() }, + { assert file("${process.out.index.get(0).get(1)}/simpleaf_index.json").exists() } + // { assert snapshot( + // path("${process.out.index.get(0).get(1)}/piscem_idx.ctab"), + // path("${process.out.index.get(0).get(1)}/piscem_idx.json"), + // path("${process.out.index.get(0).get(1)}/piscem_idx_cfish.json"), + // process.out.versions) + // .match() } + ) + } + } + + test("Homo sapiens - probe index - direct - probe csv") { + when { + process { + """ + probe_csv = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv', checkIfExists: true) + meta = [ 'id': 'CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set'] + + input[0] = Channel.of([[],[],[]]) + input[1] = Channel.of([[],[]]) + input[2] = Channel.of([ meta, probe_csv ]) + input[3] = Channel.of([[],[]]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx_cfish.json").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.ctab").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.ectab").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.json").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.refinfo").exists() }, + { assert file("${process.out.index.get(0).get(1)}/piscem_idx.sshash").exists() }, + { assert file("${process.out.index.get(0).get(1)}/simpleaf_index.json").exists() } + // { assert snapshot( + // path("${process.out.index.get(0).get(1)}/piscem_idx.ctab"), + // path("${process.out.index.get(0).get(1)}/piscem_idx.json"), + // path("${process.out.index.get(0).get(1)}/piscem_idx_cfish.json"), + // process.out.versions) + // .match() } + ) + } + } + + test("Homo sapiens - feature index - direct - feature csv") { + when { + process { + """ + feature_csv = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv', checkIfExists: true) + meta = [ 'id': 'sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref'] + + input[0] = Channel.of([[],[],[]]) + input[1] = Channel.of([[],[]]) + input[2] = Channel.of([[],[]]) + input[3] = Channel.of([ meta, feature_csv ]) """ } } @@ -90,7 +166,9 @@ nextflow_process { meta = [ 'id': 'human_transcriptome'] input[0] = Channel.of([[],[],[]]) - input[1] = Channel.of([ meta, transcriptome_fasta ]) + input[1] = Channel.of([ [], [] ]) + input[2] = Channel.of([ [], [] ]) + input[3] = Channel.of([ [], [] ]) """ } } diff --git a/modules/nf-core/simpleaf/index/tests/main.nf.test.snap b/modules/nf-core/simpleaf/index/tests/main.nf.test.snap index 5725a9356a5..af249676502 100644 --- a/modules/nf-core/simpleaf/index/tests/main.nf.test.snap +++ b/modules/nf-core/simpleaf/index/tests/main.nf.test.snap @@ -1,24 +1,48 @@ { + "Homo sapiens - probe index - direct - probe csv": { + "content": [ + [ + "versions.yml:md5,d2fa3ef3c792f5bd01cf4e05866caceb" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-02-04T20:19:57.286321286" + }, "Homo sapiens - transcriptome index - direct - transcriptome fasta": { "content": [ [ - "versions.yml:md5,bd96efe900339c637533c40b37fa5cfc" + "versions.yml:md5,d2fa3ef3c792f5bd01cf4e05866caceb" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-02-04T20:15:47.68048376" + }, + "Homo sapiens - feature index - direct - feature csv": { + "content": [ + [ + "versions.yml:md5,d2fa3ef3c792f5bd01cf4e05866caceb" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-23T00:40:55.088252924" + "timestamp": "2025-02-04T20:20:04.705227496" }, "Homo sapiens - transcriptome index - direct - transcriptome fasta - stub": { "content": [ { "0": [ [ - [ - - ], + { + "id": "stub" + }, [ "piscem_idx.ectab:md5,d41d8cd98f00b204e9800998ecf8427e", "piscem_idx.sshash:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -28,9 +52,9 @@ ], "1": [ [ - [ - - ], + { + "id": "stub" + }, [ "roers_ref.fa:md5,d41d8cd98f00b204e9800998ecf8427e", "t2g_3col.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -39,20 +63,20 @@ ], "2": [ [ - [ - - ], + { + "id": "stub" + }, "t2g_3col.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ - "versions.yml:md5,78f7da1109cf98d7b9107222704848e1" + "versions.yml:md5,70c02c3b43e257fa1abb47cb6879f6b7" ], "index": [ [ - [ - - ], + { + "id": "stub" + }, [ "piscem_idx.ectab:md5,d41d8cd98f00b204e9800998ecf8427e", "piscem_idx.sshash:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -62,9 +86,9 @@ ], "ref": [ [ - [ - - ], + { + "id": "stub" + }, [ "roers_ref.fa:md5,d41d8cd98f00b204e9800998ecf8427e", "t2g_3col.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -73,14 +97,14 @@ ], "t2g": [ [ - [ - - ], + { + "id": "stub" + }, "t2g_3col.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,78f7da1109cf98d7b9107222704848e1" + "versions.yml:md5,70c02c3b43e257fa1abb47cb6879f6b7" ] } ], @@ -88,18 +112,18 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-23T02:08:51.588975264" + "timestamp": "2025-02-04T20:20:12.01549861" }, "Homo sapiens - genome index - expanded - fasta + gtf": { "content": [ [ - "versions.yml:md5,bd96efe900339c637533c40b37fa5cfc" + "versions.yml:md5,d2fa3ef3c792f5bd01cf4e05866caceb" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-23T00:40:41.692166586" + "timestamp": "2025-02-04T20:15:30.566784151" } } \ No newline at end of file diff --git a/modules/nf-core/simpleaf/quant/environment.yml b/modules/nf-core/simpleaf/quant/environment.yml index 7e7a1020431..9053723238e 100644 --- a/modules/nf-core/simpleaf/quant/environment.yml +++ b/modules/nf-core/simpleaf/quant/environment.yml @@ -1,9 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - bioconda - conda-forge dependencies: - bioconda::alevin-fry=0.11.1 - - bioconda::piscem=0.11.0 + - bioconda::piscem=0.12.2 - bioconda::salmon=1.10.3 - - bioconda::simpleaf=0.18.4 + - bioconda::simpleaf=0.19.1 diff --git a/modules/nf-core/simpleaf/quant/main.nf b/modules/nf-core/simpleaf/quant/main.nf index 818f514b53d..58a0a015b26 100644 --- a/modules/nf-core/simpleaf/quant/main.nf +++ b/modules/nf-core/simpleaf/quant/main.nf @@ -4,8 +4,8 @@ process SIMPLEAF_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/simpleaf:0.18.4--ha6fb395_1': - 'biocontainers/simpleaf:0.18.4--ha6fb395_1' }" + 'https://depot.galaxyproject.org/singularity/simpleaf:0.19.1--ha6fb395_0': + 'biocontainers/simpleaf:0.19.1--ha6fb395_0' }" input: // @@ -53,6 +53,7 @@ process SIMPLEAF_QUANT { --resolution ${resolution} \\ --output ${prefix} \\ --threads ${task.cpus} \\ + --anndata-out \\ ${cf_option} \\ ${args} diff --git a/modules/nf-core/simpleaf/quant/tests/main.nf.test b/modules/nf-core/simpleaf/quant/tests/main.nf.test index f4cdfc1edda..b0e3e164135 100644 --- a/modules/nf-core/simpleaf/quant/tests/main.nf.test +++ b/modules/nf-core/simpleaf/quant/tests/main.nf.test @@ -23,6 +23,8 @@ nextflow_process { input[0] = Channel.of([meta, genome_fasta, gtf]) input[1] = Channel.of([[],[]]) + input[2] = Channel.of([[],[]]) + input[3] = Channel.of([[],[]]) """ } } @@ -64,6 +66,7 @@ nextflow_process { { assert file("${process.out.quant.get(0).get(1)}/alevin/quants_mat.mtx").exists() }, { assert file("${process.out.quant.get(0).get(1)}/alevin/quants_mat_cols.txt").exists() }, { assert file("${process.out.quant.get(0).get(1)}/alevin/quants_mat_rows.txt").exists() }, + { assert file("${process.out.quant.get(0).get(1)}/alevin/quants.h5ad").exists() }, // { assert snapshot( // process.out.versions, // path("${process.out.map.get(0).get(1)}/map.rad"), diff --git a/modules/nf-core/simpleaf/quant/tests/main.nf.test.snap b/modules/nf-core/simpleaf/quant/tests/main.nf.test.snap index 874b8151bfa..151e625d41f 100644 --- a/modules/nf-core/simpleaf/quant/tests/main.nf.test.snap +++ b/modules/nf-core/simpleaf/quant/tests/main.nf.test.snap @@ -32,7 +32,7 @@ ] ], "2": [ - "versions.yml:md5,c9a934ed7c246bef3ccccab002db043b" + "versions.yml:md5,9ef74a14f1fe56483b4596169f4886db" ], "map": [ [ @@ -64,7 +64,7 @@ ] ], "versions": [ - "versions.yml:md5,c9a934ed7c246bef3ccccab002db043b" + "versions.yml:md5,9ef74a14f1fe56483b4596169f4886db" ] } ], @@ -72,18 +72,18 @@ "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-23T02:00:35.55447474" + "timestamp": "2025-02-04T20:20:41.988621322" }, "test_simpleaf_quant": { "content": [ [ - "versions.yml:md5,c9a934ed7c246bef3ccccab002db043b" + "versions.yml:md5,9ef74a14f1fe56483b4596169f4886db" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-23T02:00:28.925349117" + "timestamp": "2025-02-04T20:20:32.847940374" } } \ No newline at end of file diff --git a/modules/nf-core/sistr/environment.yml b/modules/nf-core/sistr/environment.yml index 4ddd5b60776..d6fda7ecb2b 100644 --- a/modules/nf-core/sistr/environment.yml +++ b/modules/nf-core/sistr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ska/fasta/environment.yml b/modules/nf-core/ska/fasta/environment.yml index eb09059fca5..7e93c4eba24 100644 --- a/modules/nf-core/ska/fasta/environment.yml +++ b/modules/nf-core/ska/fasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::ska=1.0" + - bioconda::ska=1.0 diff --git a/modules/nf-core/ska/fasta/meta.yml b/modules/nf-core/ska/fasta/meta.yml index 407d0ac7713..603c73f3d3f 100644 --- a/modules/nf-core/ska/fasta/meta.yml +++ b/modules/nf-core/ska/fasta/meta.yml @@ -15,7 +15,7 @@ tools: documentation: "https://github.com/simonrharris/SKA/wiki" tool_dev_url: "https://github.com/simonrharris/SKA" doi: "10.1101/453142" - licence: ['MIT'] + licence: ["MIT"] input: - - meta: @@ -35,20 +35,20 @@ input: pattern: "*.txt" output: - skf: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - "*.skf": - type: file - description: File containing genome sketch - pattern: "*.skf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.skf": + type: file + description: File containing genome sketch + pattern: "*.skf" - versions: - - "versions.yml": - type: file - description: File containing software versions - pattern: "versions.yml" + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@itrujnara" diff --git a/modules/nf-core/slimfastq/environment.yml b/modules/nf-core/slimfastq/environment.yml index cafcb690d54..9914fed4949 100644 --- a/modules/nf-core/slimfastq/environment.yml +++ b/modules/nf-core/slimfastq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/smncopynumbercaller/environment.yml b/modules/nf-core/smncopynumbercaller/environment.yml index afbc4007691..6102e633301 100644 --- a/modules/nf-core/smncopynumbercaller/environment.yml +++ b/modules/nf-core/smncopynumbercaller/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/smoothxg/environment.yml b/modules/nf-core/smoothxg/environment.yml index 1e49e2cf889..2e7bd095212 100644 --- a/modules/nf-core/smoothxg/environment.yml +++ b/modules/nf-core/smoothxg/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/smoove/call/environment.yml b/modules/nf-core/smoove/call/environment.yml index 39632516a58..c8f522acba4 100644 --- a/modules/nf-core/smoove/call/environment.yml +++ b/modules/nf-core/smoove/call/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snakemake/environment.yml b/modules/nf-core/snakemake/environment.yml index e306cbd1073..39223df49ef 100644 --- a/modules/nf-core/snakemake/environment.yml +++ b/modules/nf-core/snakemake/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snapaligner/align/environment.yml b/modules/nf-core/snapaligner/align/environment.yml index 8324d125823..c2bd7a6a148 100644 --- a/modules/nf-core/snapaligner/align/environment.yml +++ b/modules/nf-core/snapaligner/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snapaligner/index/environment.yml b/modules/nf-core/snapaligner/index/environment.yml index 8324d125823..c2bd7a6a148 100644 --- a/modules/nf-core/snapaligner/index/environment.yml +++ b/modules/nf-core/snapaligner/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml index b3d97d0e846..4b2bbc7c958 100644 --- a/modules/nf-core/sniffles/environment.yml +++ b/modules/nf-core/sniffles/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snippy/core/environment.yml b/modules/nf-core/snippy/core/environment.yml index e0f44bc81f4..114a47f15bb 100644 --- a/modules/nf-core/snippy/core/environment.yml +++ b/modules/nf-core/snippy/core/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snippy/run/environment.yml b/modules/nf-core/snippy/run/environment.yml index e0f44bc81f4..114a47f15bb 100644 --- a/modules/nf-core/snippy/run/environment.yml +++ b/modules/nf-core/snippy/run/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpdists/environment.yml b/modules/nf-core/snpdists/environment.yml index 71c52aacf18..6ea1558b325 100644 --- a/modules/nf-core/snpdists/environment.yml +++ b/modules/nf-core/snpdists/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml index f2ad925161e..48236b6f011 100644 --- a/modules/nf-core/snpeff/download/environment.yml +++ b/modules/nf-core/snpeff/download/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/environment.yml b/modules/nf-core/snpeff/environment.yml index 6ac55ab765a..267ed76a95f 100644 --- a/modules/nf-core/snpeff/environment.yml +++ b/modules/nf-core/snpeff/environment.yml @@ -1,5 +1,5 @@ -# You can use this file to create a conda environment for this module: -# conda env create -f environment.yml +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index f2ad925161e..48236b6f011 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpsift/annotate/environment.yml b/modules/nf-core/snpsift/annotate/environment.yml index f38678bf7ef..fc06ffc715c 100644 --- a/modules/nf-core/snpsift/annotate/environment.yml +++ b/modules/nf-core/snpsift/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpsift/dbnsfp/environment.yml b/modules/nf-core/snpsift/dbnsfp/environment.yml index f38678bf7ef..fc06ffc715c 100644 --- a/modules/nf-core/snpsift/dbnsfp/environment.yml +++ b/modules/nf-core/snpsift/dbnsfp/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpsift/split/environment.yml b/modules/nf-core/snpsift/split/environment.yml index 931bc9093f5..c3172c350ea 100644 --- a/modules/nf-core/snpsift/split/environment.yml +++ b/modules/nf-core/snpsift/split/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpsites/environment.yml b/modules/nf-core/snpsites/environment.yml index 642d9a79c96..d6bb02c05b6 100644 --- a/modules/nf-core/snpsites/environment.yml +++ b/modules/nf-core/snpsites/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/somalier/ancestry/environment.yml b/modules/nf-core/somalier/ancestry/environment.yml index 783e5d8d162..d0f10fac8c9 100644 --- a/modules/nf-core/somalier/ancestry/environment.yml +++ b/modules/nf-core/somalier/ancestry/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index d6ce68f6ece..80eb6a006a4 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml index d6ce68f6ece..80eb6a006a4 100644 --- a/modules/nf-core/somalier/relate/environment.yml +++ b/modules/nf-core/somalier/relate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index fab44081fa2..f422ff438d7 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sourcepredict/environment.yml b/modules/nf-core/sourcepredict/environment.yml index 29ce8ea5cd7..1b73065ad2a 100644 --- a/modules/nf-core/sourcepredict/environment.yml +++ b/modules/nf-core/sourcepredict/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sourcepredict=0.5.1" + - bioconda::sourcepredict=0.5.1 diff --git a/modules/nf-core/sourmash/compare/environment.yml b/modules/nf-core/sourmash/compare/environment.yml index 25e14afa58c..fed3dfb3d2b 100644 --- a/modules/nf-core/sourmash/compare/environment.yml +++ b/modules/nf-core/sourmash/compare/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sourmash/gather/environment.yml b/modules/nf-core/sourmash/gather/environment.yml index 25e14afa58c..fed3dfb3d2b 100644 --- a/modules/nf-core/sourmash/gather/environment.yml +++ b/modules/nf-core/sourmash/gather/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sourmash/index/environment.yml b/modules/nf-core/sourmash/index/environment.yml index 25e14afa58c..fed3dfb3d2b 100644 --- a/modules/nf-core/sourmash/index/environment.yml +++ b/modules/nf-core/sourmash/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sourmash/sketch/environment.yml b/modules/nf-core/sourmash/sketch/environment.yml index 25e14afa58c..fed3dfb3d2b 100644 --- a/modules/nf-core/sourmash/sketch/environment.yml +++ b/modules/nf-core/sourmash/sketch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sourmash/taxannotate/environment.yml b/modules/nf-core/sourmash/taxannotate/environment.yml index 25e14afa58c..fed3dfb3d2b 100644 --- a/modules/nf-core/sourmash/taxannotate/environment.yml +++ b/modules/nf-core/sourmash/taxannotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/spades/environment.yml b/modules/nf-core/spades/environment.yml index 8cc5321fd3e..8f60a307f99 100644 --- a/modules/nf-core/spades/environment.yml +++ b/modules/nf-core/spades/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/spatyper/environment.yml b/modules/nf-core/spatyper/environment.yml index cbe256c5a97..7b76a600246 100644 --- a/modules/nf-core/spatyper/environment.yml +++ b/modules/nf-core/spatyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/splitubam/environment.yml b/modules/nf-core/splitubam/environment.yml index 382f9112c4e..acb62008a96 100644 --- a/modules/nf-core/splitubam/environment.yml +++ b/modules/nf-core/splitubam/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::splitubam=0.1.1" + - bioconda::splitubam=0.1.1 diff --git a/modules/nf-core/spotiflow/environment.yml b/modules/nf-core/spotiflow/environment.yml index 5a69c468fc9..8c2637dd36e 100644 --- a/modules/nf-core/spotiflow/environment.yml +++ b/modules/nf-core/spotiflow/environment.yml @@ -1,13 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - pytorch - conda-forge # NOTE https://github.com/nf-core/modules/issues/5813 dependencies: + - cpuonly - python=3.9 - pytorch - torchvision - - cpuonly - # - git FIXME necessary for "git+https://github.com/weigertlab/spotiflow@0.3.0" - # NOTE https://github.com/nf-core/modules/issues/5814 - pip: - spotiflow diff --git a/modules/nf-core/spring/compress/environment.yml b/modules/nf-core/spring/compress/environment.yml index abeb16b095c..2e0329f7b43 100644 --- a/modules/nf-core/spring/compress/environment.yml +++ b/modules/nf-core/spring/compress/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/spring/decompress/environment.yml b/modules/nf-core/spring/decompress/environment.yml index abeb16b095c..2e0329f7b43 100644 --- a/modules/nf-core/spring/decompress/environment.yml +++ b/modules/nf-core/spring/decompress/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml index 970dfbc0de7..fb68c07caa8 100644 --- a/modules/nf-core/sratools/fasterqdump/environment.yml +++ b/modules/nf-core/sratools/fasterqdump/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml index 6596bc7cf74..22b622b9abe 100644 --- a/modules/nf-core/sratools/prefetch/environment.yml +++ b/modules/nf-core/sratools/prefetch/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/srst2/srst2/environment.yml b/modules/nf-core/srst2/srst2/environment.yml index ecce1cf9726..6fb67837b2b 100644 --- a/modules/nf-core/srst2/srst2/environment.yml +++ b/modules/nf-core/srst2/srst2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ssuissero/environment.yml b/modules/nf-core/ssuissero/environment.yml index 042a9c5b03f..63646c7da88 100644 --- a/modules/nf-core/ssuissero/environment.yml +++ b/modules/nf-core/ssuissero/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stadeniolib/scramble/environment.yml b/modules/nf-core/stadeniolib/scramble/environment.yml index da097f41864..dae883daff7 100644 --- a/modules/nf-core/stadeniolib/scramble/environment.yml +++ b/modules/nf-core/stadeniolib/scramble/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/staphopiasccmec/environment.yml b/modules/nf-core/staphopiasccmec/environment.yml index fc31f4bc270..c98e6b2b6a7 100644 --- a/modules/nf-core/staphopiasccmec/environment.yml +++ b/modules/nf-core/staphopiasccmec/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 9ed1940faac..91e37ae12e1 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 9ed1940faac..91e37ae12e1 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/star/starsolo/environment.yml b/modules/nf-core/star/starsolo/environment.yml index 9ed1940faac..91e37ae12e1 100644 --- a/modules/nf-core/star/starsolo/environment.yml +++ b/modules/nf-core/star/starsolo/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/staramr/search/environment.yml b/modules/nf-core/staramr/search/environment.yml index c90c2637db1..683832bd9ea 100644 --- a/modules/nf-core/staramr/search/environment.yml +++ b/modules/nf-core/staramr/search/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stardist/environment.yml b/modules/nf-core/stardist/environment.yml index 33c9530f40f..da94471cd2e 100644 --- a/modules/nf-core/stardist/environment.yml +++ b/modules/nf-core/stardist/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stecfinder/environment.yml b/modules/nf-core/stecfinder/environment.yml index d533f168fed..4451180691f 100644 --- a/modules/nf-core/stecfinder/environment.yml +++ b/modules/nf-core/stecfinder/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stitch/environment.yml b/modules/nf-core/stitch/environment.yml index 4978bec281f..7009e731ec9 100644 --- a/modules/nf-core/stitch/environment.yml +++ b/modules/nf-core/stitch/environment.yml @@ -1,8 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + - bioconda::htslib=1.18 + - bioconda::r-stitch=1.6.10 - conda-forge::r-base=4.3.1 - conda-forge::rsync=3.2.7 - - bioconda::r-stitch=1.6.10 - - bioconda::htslib=1.18 diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml index c476e2b3674..3a9067a094c 100644 --- a/modules/nf-core/stranger/environment.yml +++ b/modules/nf-core/stranger/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml index 052c6baa5f3..33edb70c4ae 100644 --- a/modules/nf-core/strelka/germline/environment.yml +++ b/modules/nf-core/strelka/germline/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml index 052c6baa5f3..33edb70c4ae 100644 --- a/modules/nf-core/strelka/somatic/environment.yml +++ b/modules/nf-core/strelka/somatic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stringtie/merge/environment.yml b/modules/nf-core/stringtie/merge/environment.yml index 0556de41a75..ef1f3d0e150 100644 --- a/modules/nf-core/stringtie/merge/environment.yml +++ b/modules/nf-core/stringtie/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 906b7486c0e..a51985b4f07 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index fdb57502009..15775250961 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index dc4e6c936a7..12a177c6ef7 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-summarizedexperiment=1.32.0" + - bioconda::bioconductor-summarizedexperiment=1.32.0 diff --git a/modules/nf-core/survivor/bedpetovcf/environment.yml b/modules/nf-core/survivor/bedpetovcf/environment.yml index ce3babdc92e..a06428dacd8 100644 --- a/modules/nf-core/survivor/bedpetovcf/environment.yml +++ b/modules/nf-core/survivor/bedpetovcf/environment.yml @@ -1,6 +1,7 @@ --- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::survivor=1.0.7" + - bioconda::survivor=1.0.7 diff --git a/modules/nf-core/survivor/filter/environment.yml b/modules/nf-core/survivor/filter/environment.yml index 6603bdcc024..a06428dacd8 100644 --- a/modules/nf-core/survivor/filter/environment.yml +++ b/modules/nf-core/survivor/filter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/survivor/merge/environment.yml b/modules/nf-core/survivor/merge/environment.yml index 6603bdcc024..a06428dacd8 100644 --- a/modules/nf-core/survivor/merge/environment.yml +++ b/modules/nf-core/survivor/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/survivor/simsv/environment.yml b/modules/nf-core/survivor/simsv/environment.yml index 6603bdcc024..a06428dacd8 100644 --- a/modules/nf-core/survivor/simsv/environment.yml +++ b/modules/nf-core/survivor/simsv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/survivor/stats/environment.yml b/modules/nf-core/survivor/stats/environment.yml index 6603bdcc024..a06428dacd8 100644 --- a/modules/nf-core/survivor/stats/environment.yml +++ b/modules/nf-core/survivor/stats/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svaba/environment.yml b/modules/nf-core/svaba/environment.yml index 2f117759947..9bc9051e471 100644 --- a/modules/nf-core/svaba/environment.yml +++ b/modules/nf-core/svaba/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svanalyzer/svbenchmark/environment.yml b/modules/nf-core/svanalyzer/svbenchmark/environment.yml index e1f68b71a30..16e093a909b 100644 --- a/modules/nf-core/svanalyzer/svbenchmark/environment.yml +++ b/modules/nf-core/svanalyzer/svbenchmark/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svdb/build/environment.yml b/modules/nf-core/svdb/build/environment.yml index 2af552205f8..2c696f4733f 100644 --- a/modules/nf-core/svdb/build/environment.yml +++ b/modules/nf-core/svdb/build/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index ab87ec70a1b..dc587136eb1 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml index 2af552205f8..2c696f4733f 100644 --- a/modules/nf-core/svdb/query/environment.yml +++ b/modules/nf-core/svdb/query/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtk/baftest/environment.yml b/modules/nf-core/svtk/baftest/environment.yml index 42aa12a2126..d349bc0ac9a 100644 --- a/modules/nf-core/svtk/baftest/environment.yml +++ b/modules/nf-core/svtk/baftest/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtk/countsvtypes/environment.yml b/modules/nf-core/svtk/countsvtypes/environment.yml index 42aa12a2126..d349bc0ac9a 100644 --- a/modules/nf-core/svtk/countsvtypes/environment.yml +++ b/modules/nf-core/svtk/countsvtypes/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtk/rdtest2vcf/environment.yml b/modules/nf-core/svtk/rdtest2vcf/environment.yml index 42aa12a2126..d349bc0ac9a 100644 --- a/modules/nf-core/svtk/rdtest2vcf/environment.yml +++ b/modules/nf-core/svtk/rdtest2vcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtk/standardize/environment.yml b/modules/nf-core/svtk/standardize/environment.yml index 42aa12a2126..d349bc0ac9a 100644 --- a/modules/nf-core/svtk/standardize/environment.yml +++ b/modules/nf-core/svtk/standardize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtk/vcf2bed/environment.yml b/modules/nf-core/svtk/vcf2bed/environment.yml index 42aa12a2126..d349bc0ac9a 100644 --- a/modules/nf-core/svtk/vcf2bed/environment.yml +++ b/modules/nf-core/svtk/vcf2bed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtools/vcftobedpe/environment.yml b/modules/nf-core/svtools/vcftobedpe/environment.yml new file mode 100644 index 00000000000..b06a00bd5be --- /dev/null +++ b/modules/nf-core/svtools/vcftobedpe/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::svtools=0.5.1" diff --git a/modules/nf-core/svtools/vcftobedpe/main.nf b/modules/nf-core/svtools/vcftobedpe/main.nf new file mode 100644 index 00000000000..98560e2a013 --- /dev/null +++ b/modules/nf-core/svtools/vcftobedpe/main.nf @@ -0,0 +1,46 @@ +process SVTOOLS_VCFTOBEDPE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/svtools:0.5.1--py_0': + 'biocontainers/svtools:0.5.1--py_0' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.bedpe"), emit: bedpe + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: "" + def prefix = task.ext.prefix ?: "${meta.id}" + """ + svtools vcftobedpe \\ + $args + --input $vcf \\ + --output ${prefix}.bedpe \\ + --tempdir ./tmp + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svtools: \$(svtools --version |& sed '1!d ; s/svtools //') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bedpe + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svtools: \$(svtools --version |& sed '1!d ; s/svtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/svtools/vcftobedpe/meta.yml b/modules/nf-core/svtools/vcftobedpe/meta.yml new file mode 100644 index 00000000000..f42dfa1a2fa --- /dev/null +++ b/modules/nf-core/svtools/vcftobedpe/meta.yml @@ -0,0 +1,49 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "svtools_vcftobedpe" +description: Convert a VCF file to a BEDPE file. +keywords: + - structural + - bedpe + - vcf + - conversion + - variants +tools: + - "svtools": + description: "Tools for processing and analyzing structural variants" + tool_dev_url: "https://github.com/hall-lab/svtools" + licence: ['MIT License'] + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: Input VCF file containing structural variants + pattern: "*.{vcf,vcf.gz}" + +output: + - bedpe: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bedpe": + type: file + description: The converted BEDPE file + pattern: "*.bedpe" + + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test new file mode 100644 index 00000000000..c5b4c2ef8de --- /dev/null +++ b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process SVTOOLS_VCFTOBEDPE" + script "../main.nf" + process "SVTOOLS_VCFTOBEDPE" + + tag "modules" + tag "modules_nfcore" + tag "svtools" + tag "svtools/vcftobedpe" + + test("homo_sapiens - vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test.snap b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test.snap new file mode 100644 index 00000000000..3299ccf560b --- /dev/null +++ b/modules/nf-core/svtools/vcftobedpe/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "homo_sapiens - vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bedpe:md5,78e3231e39d534d26ba32f64f8f5e094" + ] + ], + "1": [ + "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8" + ], + "bedpe": [ + [ + { + "id": "test" + }, + "test.bedpe:md5,78e3231e39d534d26ba32f64f8f5e094" + ] + ], + "versions": [ + "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-06T16:08:14.1286306" + }, + "homo_sapiens - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8" + ], + "bedpe": [ + [ + { + "id": "test" + }, + "test.bedpe:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1af4f5a32bfc89f4d6d6c94cf1d4afd8" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-06T16:08:21.008497589" + } +} \ No newline at end of file diff --git a/modules/nf-core/svtyper/svtyper/environment.yml b/modules/nf-core/svtyper/svtyper/environment.yml index c173b433910..314c7e48209 100644 --- a/modules/nf-core/svtyper/svtyper/environment.yml +++ b/modules/nf-core/svtyper/svtyper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/svtyper/svtypersso/environment.yml b/modules/nf-core/svtyper/svtypersso/environment.yml index c9b7d5450d1..6d3fddf1bea 100644 --- a/modules/nf-core/svtyper/svtypersso/environment.yml +++ b/modules/nf-core/svtyper/svtypersso/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::svtyper=0.7.1" + - bioconda::svtyper=0.7.1 diff --git a/modules/nf-core/svync/environment.yml b/modules/nf-core/svync/environment.yml index dbdfe4bbd82..cada6309943 100644 --- a/modules/nf-core/svync/environment.yml +++ b/modules/nf-core/svync/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::svync=0.1.2" + - bioconda::svync=0.1.2 diff --git a/modules/nf-core/sylph/profile/environment.yml b/modules/nf-core/sylph/profile/environment.yml new file mode 100644 index 00000000000..ae8337cc8b8 --- /dev/null +++ b/modules/nf-core/sylph/profile/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::sylph=0.7.0 diff --git a/modules/nf-core/sylph/profile/main.nf b/modules/nf-core/sylph/profile/main.nf new file mode 100644 index 00000000000..ae85e9198fd --- /dev/null +++ b/modules/nf-core/sylph/profile/main.nf @@ -0,0 +1,49 @@ +process SYLPH_PROFILE { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/sylph:0.7.0--h919a2d8_0' : + 'biocontainers/sylph:0.7.0--h919a2d8_0' }" + + input: + tuple val(meta), path(reads) + path(database) + + output: + tuple val(meta), path('*.tsv'), emit: profile_out + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + sylph profile \\ + -t $task.cpus \\ + $args \\ + $reads \\ + $database\\ + -o ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sylph: \$(sylph -V | awk '{print \$2}') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sylph: \$(sylph -V | awk '{print \$2}') + END_VERSIONS + """ + +} diff --git a/modules/nf-core/sylph/profile/meta.yml b/modules/nf-core/sylph/profile/meta.yml new file mode 100644 index 00000000000..ce41070719c --- /dev/null +++ b/modules/nf-core/sylph/profile/meta.yml @@ -0,0 +1,51 @@ +name: "sylph_profile" +description: Sylph profile command for taxonoming profiling +keywords: + - profile + - metagenomics + - sylph + - classification +tools: + - sylph: + description: Sylph quickly enables querying of genomes against even low-coverage + shotgun metagenomes to find nearest neighbour ANI. + homepage: https://github.com/bluenote-1577/sylph + documentation: https://github.com/bluenote-1577/sylph + tool_dev_url: https://github.com/bluenote-1577/sylph + doi: 10.1038/s41587-024-02412-y + licence: ["MIT"] + identifier: biotools:sylph +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: | + List of input FastQ/FASTA files of size 1 and 2 for single-end and paired-end data, + respectively. They are automatically sketched to .sylsp/.syldb + - - database: + type: file + description: Pre-sketched *.syldb/*.sylsp files. Raw single-end fastq/fasta are allowed and will be automatically sketched to .sylsp/.syldb. + pattern: "*.{syldb,sylsp,fasta,fastq}" +output: + - profile_out: + - meta: + type: map + description: Groovy Map containing sample information + - "*.tsv": + type: file + description: Output file of species-level taxonomic profiling with abundances and ANIs. + pattern: "*tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jiahang1234" + - "@sofstam" +maintainers: + - "@sofstam" diff --git a/modules/nf-core/sylph/profile/tests/main.nf.test b/modules/nf-core/sylph/profile/tests/main.nf.test new file mode 100644 index 00000000000..8d1993e20ec --- /dev/null +++ b/modules/nf-core/sylph/profile/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process SYLPH_PROFILE" + script "../main.nf" + process "SYLPH_PROFILE" + tag "modules" + tag "modules_nfcore" + tag "sylph" + tag "sylph/profile" + + test("sarscov2 illumina single-end [fastq_gz]") { + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + """ + } + } + + then { + assert process.success + assert snapshot( + process.out.versions, + file(process.out.profile_out[0][1]).readLines()[0] + ).match() + } + } + + test("sarscov2 illumina paired-end [fastq_gz]") { + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + """ + } + } + + then { + assert process.success + assert snapshot( + process.out.versions, + file(process.out.profile_out[0][1]).readLines()[0] + ).match() + } + } + + test("sarscov2 illumina paired-end [fastq_gz]-stub") { + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path +'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + } +} diff --git a/modules/nf-core/sylph/profile/tests/main.nf.test.snap b/modules/nf-core/sylph/profile/tests/main.nf.test.snap new file mode 100644 index 00000000000..d7a487c401e --- /dev/null +++ b/modules/nf-core/sylph/profile/tests/main.nf.test.snap @@ -0,0 +1,61 @@ +{ + "sarscov2 illumina paired-end [fastq_gz]": { + "content": [ + [ + "versions.yml:md5,7b5a545483277cc0ff9189f8891e737f" + ], + "Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-27T15:47:59.374481624" + }, + "sarscov2 illumina single-end [fastq_gz]": { + "content": [ + [ + "versions.yml:md5,7b5a545483277cc0ff9189f8891e737f" + ], + "Sample_file\tGenome_file\tTaxonomic_abundance\tSequence_abundance\tAdjusted_ANI\tEff_cov\tANI_5-95_percentile\tEff_lambda\tLambda_5-95_percentile\tMedian_cov\tMean_cov_geq1\tContainment_ind\tNaive_ANI\tkmers_reassigned\tContig_name" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-27T15:47:53.556942841" + }, + "sarscov2 illumina paired-end [fastq_gz]-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,7b5a545483277cc0ff9189f8891e737f" + ], + "profile_out": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7b5a545483277cc0ff9189f8891e737f" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-27T15:48:04.991824868" + } +} \ No newline at end of file diff --git a/modules/nf-core/sylph/sketch/environment.yml b/modules/nf-core/sylph/sketch/environment.yml index f8d852d471a..ae8337cc8b8 100644 --- a/modules/nf-core/sylph/sketch/environment.yml +++ b/modules/nf-core/sylph/sketch/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::sylph=0.7.0" + - bioconda::sylph=0.7.0 diff --git a/modules/nf-core/sylph/sketch/meta.yml b/modules/nf-core/sylph/sketch/meta.yml index 7a9abdf85b1..a7278db68be 100644 --- a/modules/nf-core/sylph/sketch/meta.yml +++ b/modules/nf-core/sylph/sketch/meta.yml @@ -34,8 +34,7 @@ output: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pattern: "my_sketches/*.sylsp" + e.g. [ id:'test'] - my_sketches/*.sylsp: type: map description: | diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 017c259da1c..fe48f5422ab 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index 017c259da1c..fe48f5422ab 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 017c259da1c..fe48f5422ab 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tailfindr/environment.yml b/modules/nf-core/tailfindr/environment.yml index 833397eac74..381157b4f9a 100644 --- a/modules/nf-core/tailfindr/environment.yml +++ b/modules/nf-core/tailfindr/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tar/environment.yml b/modules/nf-core/tar/environment.yml index 1decc62432d..57c48e9aa93 100644 --- a/modules/nf-core/tar/environment.yml +++ b/modules/nf-core/tar/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/taxonkit/lineage/environment.yml b/modules/nf-core/taxonkit/lineage/environment.yml index e68c6d6e46d..febd82152d1 100644 --- a/modules/nf-core/taxonkit/lineage/environment.yml +++ b/modules/nf-core/taxonkit/lineage/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::taxonkit=0.18.0" + - bioconda::taxonkit=0.18.0 diff --git a/modules/nf-core/taxonkit/name2taxid/environment.yml b/modules/nf-core/taxonkit/name2taxid/environment.yml index 37c42979ba4..dfcb809e00d 100644 --- a/modules/nf-core/taxonkit/name2taxid/environment.yml +++ b/modules/nf-core/taxonkit/name2taxid/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::taxonkit=0.15.1" + - bioconda::taxonkit=0.15.1 diff --git a/modules/nf-core/taxpasta/merge/environment.yml b/modules/nf-core/taxpasta/merge/environment.yml index eb48f436582..755d1bc7041 100644 --- a/modules/nf-core/taxpasta/merge/environment.yml +++ b/modules/nf-core/taxpasta/merge/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/taxpasta/standardise/environment.yml b/modules/nf-core/taxpasta/standardise/environment.yml index eb48f436582..755d1bc7041 100644 --- a/modules/nf-core/taxpasta/standardise/environment.yml +++ b/modules/nf-core/taxpasta/standardise/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tbprofiler/profile/environment.yml b/modules/nf-core/tbprofiler/profile/environment.yml index 3185d0c187f..04b40ecd143 100644 --- a/modules/nf-core/tbprofiler/profile/environment.yml +++ b/modules/nf-core/tbprofiler/profile/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/align/environment.yml b/modules/nf-core/tcoffee/align/environment.yml index 26a17e70983..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/align/environment.yml +++ b/modules/nf-core/tcoffee/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/alncompare/environment.yml b/modules/nf-core/tcoffee/alncompare/environment.yml index 26a17e70983..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/alncompare/environment.yml +++ b/modules/nf-core/tcoffee/alncompare/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/consensus/environment.yml b/modules/nf-core/tcoffee/consensus/environment.yml index 26a17e70983..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/consensus/environment.yml +++ b/modules/nf-core/tcoffee/consensus/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/extractfrompdb/environment.yml b/modules/nf-core/tcoffee/extractfrompdb/environment.yml index 7cc504fcaa0..9feadcf3c08 100644 --- a/modules/nf-core/tcoffee/extractfrompdb/environment.yml +++ b/modules/nf-core/tcoffee/extractfrompdb/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/irmsd/environment.yml b/modules/nf-core/tcoffee/irmsd/environment.yml index 26a17e70983..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/irmsd/environment.yml +++ b/modules/nf-core/tcoffee/irmsd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/regressive/environment.yml b/modules/nf-core/tcoffee/regressive/environment.yml index 26a17e70983..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/regressive/environment.yml +++ b/modules/nf-core/tcoffee/regressive/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/seqreformat/environment.yml b/modules/nf-core/tcoffee/seqreformat/environment.yml index 7cc504fcaa0..9feadcf3c08 100644 --- a/modules/nf-core/tcoffee/seqreformat/environment.yml +++ b/modules/nf-core/tcoffee/seqreformat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml index 615d140e6bb..c17fbb8f14e 100644 --- a/modules/nf-core/tcoffee/tcs/environment.yml +++ b/modules/nf-core/tcoffee/tcs/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::t-coffee=13.46.0.919e8c6b" + - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/telseq/environment.yml b/modules/nf-core/telseq/environment.yml index 5502308b97c..384d0c2baac 100644 --- a/modules/nf-core/telseq/environment.yml +++ b/modules/nf-core/telseq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/thermorawfileparser/environment.yml b/modules/nf-core/thermorawfileparser/environment.yml index e7bfd0b107f..79890633a35 100644 --- a/modules/nf-core/thermorawfileparser/environment.yml +++ b/modules/nf-core/thermorawfileparser/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::thermorawfileparser=1.4.3" + - bioconda::thermorawfileparser=1.4.3 diff --git a/modules/nf-core/tiara/tiara/environment.yml b/modules/nf-core/tiara/tiara/environment.yml index 2fc0d365749..ccfc8af7f2d 100644 --- a/modules/nf-core/tiara/tiara/environment.yml +++ b/modules/nf-core/tiara/tiara/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index 2fd01cfd4b9..a33b14c85fa 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index 2fd01cfd4b9..a33b14c85fa 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tidk/explore/environment.yml b/modules/nf-core/tidk/explore/environment.yml index 22eb538bcfb..5e74a9a2f27 100644 --- a/modules/nf-core/tidk/explore/environment.yml +++ b/modules/nf-core/tidk/explore/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::tidk=0.2.41" + - bioconda::tidk=0.2.41 diff --git a/modules/nf-core/tidk/plot/environment.yml b/modules/nf-core/tidk/plot/environment.yml index 22eb538bcfb..5e74a9a2f27 100644 --- a/modules/nf-core/tidk/plot/environment.yml +++ b/modules/nf-core/tidk/plot/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::tidk=0.2.41" + - bioconda::tidk=0.2.41 diff --git a/modules/nf-core/tidk/search/environment.yml b/modules/nf-core/tidk/search/environment.yml index 22eb538bcfb..5e74a9a2f27 100644 --- a/modules/nf-core/tidk/search/environment.yml +++ b/modules/nf-core/tidk/search/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::tidk=0.2.41" + - bioconda::tidk=0.2.41 diff --git a/modules/nf-core/topas/gencons/environment.yml b/modules/nf-core/topas/gencons/environment.yml index 83e393086b3..a593fcffe13 100644 --- a/modules/nf-core/topas/gencons/environment.yml +++ b/modules/nf-core/topas/gencons/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/toulligqc/environment.yml b/modules/nf-core/toulligqc/environment.yml index 2d160afe2da..e1632a8b342 100644 --- a/modules/nf-core/toulligqc/environment.yml +++ b/modules/nf-core/toulligqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::toulligqc=2.5.6" + - bioconda::toulligqc=2.5.6 diff --git a/modules/nf-core/transdecoder/longorf/environment.yml b/modules/nf-core/transdecoder/longorf/environment.yml index 19be873fc94..ffe26853926 100644 --- a/modules/nf-core/transdecoder/longorf/environment.yml +++ b/modules/nf-core/transdecoder/longorf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/transdecoder/predict/environment.yml b/modules/nf-core/transdecoder/predict/environment.yml index 2484d15af09..4731c650b0c 100644 --- a/modules/nf-core/transdecoder/predict/environment.yml +++ b/modules/nf-core/transdecoder/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml index 53b88a1fbd6..130e343c5bf 100644 --- a/modules/nf-core/trgt/genotype/environment.yml +++ b/modules/nf-core/trgt/genotype/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.5.0" + - bioconda::trgt=1.5.0 diff --git a/modules/nf-core/trgt/merge/environment.yml b/modules/nf-core/trgt/merge/environment.yml index 1f49dba6b3a..130e343c5bf 100644 --- a/modules/nf-core/trgt/merge/environment.yml +++ b/modules/nf-core/trgt/merge/environment.yml @@ -1,6 +1,7 @@ +--- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.5.0" + - bioconda::trgt=1.5.0 diff --git a/modules/nf-core/trgt/plot/environment.yml b/modules/nf-core/trgt/plot/environment.yml index 1f49dba6b3a..130e343c5bf 100644 --- a/modules/nf-core/trgt/plot/environment.yml +++ b/modules/nf-core/trgt/plot/environment.yml @@ -1,6 +1,7 @@ +--- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::trgt=1.5.0" + - bioconda::trgt=1.5.0 diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index b1efd94c4a0..568b9e72efa 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/trimmomatic/environment.yml b/modules/nf-core/trimmomatic/environment.yml index ab4b72b77a4..994bfd5ab35 100644 --- a/modules/nf-core/trimmomatic/environment.yml +++ b/modules/nf-core/trimmomatic/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/trinity/environment.yml b/modules/nf-core/trinity/environment.yml index 158e27817b1..68656e74498 100644 --- a/modules/nf-core/trinity/environment.yml +++ b/modules/nf-core/trinity/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/trust4/environment.yml b/modules/nf-core/trust4/environment.yml index 7e07e377e55..2841bc953f5 100644 --- a/modules/nf-core/trust4/environment.yml +++ b/modules/nf-core/trust4/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trust4=1.0.13" + - bioconda::trust4=1.0.13 diff --git a/modules/nf-core/truvari/bench/environment.yml b/modules/nf-core/truvari/bench/environment.yml index 7c5429e003b..cbc6ac8a693 100644 --- a/modules/nf-core/truvari/bench/environment.yml +++ b/modules/nf-core/truvari/bench/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/truvari/consistency/environment.yml b/modules/nf-core/truvari/consistency/environment.yml index 0844cd49096..cbc6ac8a693 100644 --- a/modules/nf-core/truvari/consistency/environment.yml +++ b/modules/nf-core/truvari/consistency/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::truvari=4.1.0" + - bioconda::truvari=4.1.0 diff --git a/modules/nf-core/truvari/segment/environment.yml b/modules/nf-core/truvari/segment/environment.yml index 0844cd49096..cbc6ac8a693 100644 --- a/modules/nf-core/truvari/segment/environment.yml +++ b/modules/nf-core/truvari/segment/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::truvari=4.1.0" + - bioconda::truvari=4.1.0 diff --git a/modules/nf-core/trycycler/cluster/environment.yml b/modules/nf-core/trycycler/cluster/environment.yml index 15112089c7e..87a6b71caef 100644 --- a/modules/nf-core/trycycler/cluster/environment.yml +++ b/modules/nf-core/trycycler/cluster/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trycycler=0.5.3" + - bioconda::trycycler=0.5.3 diff --git a/modules/nf-core/trycycler/subsample/environment.yml b/modules/nf-core/trycycler/subsample/environment.yml index 15112089c7e..87a6b71caef 100644 --- a/modules/nf-core/trycycler/subsample/environment.yml +++ b/modules/nf-core/trycycler/subsample/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::trycycler=0.5.3" + - bioconda::trycycler=0.5.3 diff --git a/modules/nf-core/tsebra/environment.yml b/modules/nf-core/tsebra/environment.yml index f189f6bda7a..4a7a6738160 100644 --- a/modules/nf-core/tsebra/environment.yml +++ b/modules/nf-core/tsebra/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::tsebra=1.1.2.5" + - bioconda::tsebra=1.1.2.5 diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 4b6df0cfe5c..9dfdbfac979 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-tximeta=1.20.1" + - bioconda::bioconductor-tximeta=1.20.1 diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 94e825f03ea..beaced44d72 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index 27868a444c5..2e853e0918d 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/bedtobigbed/environment.yml b/modules/nf-core/ucsc/bedtobigbed/environment.yml index 62670c4eba4..d7b6802eab2 100644 --- a/modules/nf-core/ucsc/bedtobigbed/environment.yml +++ b/modules/nf-core/ucsc/bedtobigbed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml b/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml index 94d3fc6053e..ddce247f0ad 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/gtftogenepred/environment.yml b/modules/nf-core/ucsc/gtftogenepred/environment.yml index 5c4f6c2fa63..86709a0d4eb 100644 --- a/modules/nf-core/ucsc/gtftogenepred/environment.yml +++ b/modules/nf-core/ucsc/gtftogenepred/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/liftover/environment.yml b/modules/nf-core/ucsc/liftover/environment.yml index db54ca2b5c9..874d15e41ba 100644 --- a/modules/nf-core/ucsc/liftover/environment.yml +++ b/modules/nf-core/ucsc/liftover/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml index 331ad3b27c4..e80eb6d092a 100644 --- a/modules/nf-core/ucsc/wigtobigwig/environment.yml +++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ultra/align/environment.yml b/modules/nf-core/ultra/align/environment.yml index 23c5097c14f..4bba7fddd0f 100644 --- a/modules/nf-core/ultra/align/environment.yml +++ b/modules/nf-core/ultra/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ultra/index/environment.yml b/modules/nf-core/ultra/index/environment.yml index 30271567b3c..00b7c24602a 100644 --- a/modules/nf-core/ultra/index/environment.yml +++ b/modules/nf-core/ultra/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ultra/pipeline/environment.yml b/modules/nf-core/ultra/pipeline/environment.yml index 30271567b3c..00b7c24602a 100644 --- a/modules/nf-core/ultra/pipeline/environment.yml +++ b/modules/nf-core/ultra/pipeline/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ultraplex/environment.yml b/modules/nf-core/ultraplex/environment.yml index 2c5b12669cf..2c97c5c705c 100644 --- a/modules/nf-core/ultraplex/environment.yml +++ b/modules/nf-core/ultraplex/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/umicollapse/environment.yml b/modules/nf-core/umicollapse/environment.yml index 066f55eef72..bbabfd56eed 100644 --- a/modules/nf-core/umicollapse/environment.yml +++ b/modules/nf-core/umicollapse/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index 9f9e03c4972..e5721f1e76b 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index 9f9e03c4972..e5721f1e76b 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/umitools/group/environment.yml b/modules/nf-core/umitools/group/environment.yml index 9f9e03c4972..e5721f1e76b 100644 --- a/modules/nf-core/umitools/group/environment.yml +++ b/modules/nf-core/umitools/group/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index 9f9e03c4972..e5721f1e76b 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/unicycler/environment.yml b/modules/nf-core/unicycler/environment.yml index bcafec00cb6..34bc8a5e452 100644 --- a/modules/nf-core/unicycler/environment.yml +++ b/modules/nf-core/unicycler/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/universc/environment.yml b/modules/nf-core/universc/environment.yml deleted file mode 100644 index 3cebeff05bf..00000000000 --- a/modules/nf-core/universc/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index ae4fa457200..9b926b1ffaf 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml index 9ed33552919..cdd3d462554 100644 --- a/modules/nf-core/untarfiles/environment.yml +++ b/modules/nf-core/untarfiles/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/unzip/environment.yml b/modules/nf-core/unzip/environment.yml index e93c649f443..2461589539a 100644 --- a/modules/nf-core/unzip/environment.yml +++ b/modules/nf-core/unzip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/unzipfiles/environment.yml b/modules/nf-core/unzipfiles/environment.yml index e93c649f443..2461589539a 100644 --- a/modules/nf-core/unzipfiles/environment.yml +++ b/modules/nf-core/unzipfiles/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/upd/environment.yml b/modules/nf-core/upd/environment.yml index 307f13b3796..a45a25cd950 100644 --- a/modules/nf-core/upd/environment.yml +++ b/modules/nf-core/upd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/upp/align/environment.yml b/modules/nf-core/upp/align/environment.yml index da0eaa9a745..7ef6e1fad4b 100644 --- a/modules/nf-core/upp/align/environment.yml +++ b/modules/nf-core/upp/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml index a835c6db4b5..7a10c540ce5 100644 --- a/modules/nf-core/vardictjava/environment.yml +++ b/modules/nf-core/vardictjava/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/variantbam/environment.yml b/modules/nf-core/variantbam/environment.yml index 3f39419da17..22d3263f700 100644 --- a/modules/nf-core/variantbam/environment.yml +++ b/modules/nf-core/variantbam/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/varlociraptor/callvariants/environment.yml b/modules/nf-core/varlociraptor/callvariants/environment.yml index 0d1519bec7c..cebb2ef3d9b 100644 --- a/modules/nf-core/varlociraptor/callvariants/environment.yml +++ b/modules/nf-core/varlociraptor/callvariants/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml b/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml index 0d1519bec7c..cebb2ef3d9b 100644 --- a/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml +++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/varlociraptor/preprocess/environment.yml b/modules/nf-core/varlociraptor/preprocess/environment.yml index 0d1519bec7c..cebb2ef3d9b 100644 --- a/modules/nf-core/varlociraptor/preprocess/environment.yml +++ b/modules/nf-core/varlociraptor/preprocess/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml index d078bfaed58..22c6b80dc52 100644 --- a/modules/nf-core/vcf2cytosure/environment.yml +++ b/modules/nf-core/vcf2cytosure/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcf2db/environment.yml b/modules/nf-core/vcf2db/environment.yml index 01fc2793871..81deb6aa6fd 100644 --- a/modules/nf-core/vcf2db/environment.yml +++ b/modules/nf-core/vcf2db/environment.yml @@ -5,12 +5,8 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=conda-forge/python - - conda-forge::python=2.7 - # renovate: datasource=conda depName=conda-forge/python-snappy - - conda-forge::python-snappy=0.5.4 - # renovate: datasource=conda depName=conda-forge/snappy - - conda-forge::snappy=1.1.8 - # renovate: datasource=conda depName=bioconda/cyvcf2 - bioconda::cyvcf2=0.20.9 - # renovate: datasource=conda depName=bioconda/vcf2db - bioconda::vcf2db=2020.02.24 + - conda-forge::python-snappy=0.5.4 + - conda-forge::python=2.7 + - conda-forge::snappy=1.1.8 diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml index b5b73f49e65..4e617a0a11c 100644 --- a/modules/nf-core/vcf2maf/environment.yml +++ b/modules/nf-core/vcf2maf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcfanno/environment.yml b/modules/nf-core/vcfanno/environment.yml index da0f73e420a..f780d24d234 100644 --- a/modules/nf-core/vcfanno/environment.yml +++ b/modules/nf-core/vcfanno/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcflib/vcfbreakmulti/environment.yml b/modules/nf-core/vcflib/vcfbreakmulti/environment.yml index e918887f9d0..cca85b1c92a 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/environment.yml +++ b/modules/nf-core/vcflib/vcfbreakmulti/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcflib/vcffilter/environment.yml b/modules/nf-core/vcflib/vcffilter/environment.yml index e918887f9d0..cca85b1c92a 100644 --- a/modules/nf-core/vcflib/vcffilter/environment.yml +++ b/modules/nf-core/vcflib/vcffilter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcflib/vcffixup/environment.yml b/modules/nf-core/vcflib/vcffixup/environment.yml index d0a99ffd761..cca85b1c92a 100644 --- a/modules/nf-core/vcflib/vcffixup/environment.yml +++ b/modules/nf-core/vcflib/vcffixup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::vcflib=1.0.3" + - bioconda::vcflib=1.0.3 diff --git a/modules/nf-core/vcflib/vcfuniq/environment.yml b/modules/nf-core/vcflib/vcfuniq/environment.yml index e918887f9d0..cca85b1c92a 100644 --- a/modules/nf-core/vcflib/vcfuniq/environment.yml +++ b/modules/nf-core/vcflib/vcfuniq/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vcftools/environment.yml b/modules/nf-core/vcftools/environment.yml index 7dcc752b86e..ff0e9d03cd3 100644 --- a/modules/nf-core/vcftools/environment.yml +++ b/modules/nf-core/vcftools/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/velocyto/environment.yml b/modules/nf-core/velocyto/environment.yml index 6c59ad55e69..f0a06a20d2a 100644 --- a/modules/nf-core/velocyto/environment.yml +++ b/modules/nf-core/velocyto/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::velocyto.py=0.17.17" + - bioconda::velocyto.py=0.17.17 diff --git a/modules/nf-core/verifybamid/verifybamid/environment.yml b/modules/nf-core/verifybamid/verifybamid/environment.yml index 6f40151d0aa..eb2ef9f745c 100644 --- a/modules/nf-core/verifybamid/verifybamid/environment.yml +++ b/modules/nf-core/verifybamid/verifybamid/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/verifybamid/verifybamid2/environment.yml b/modules/nf-core/verifybamid/verifybamid2/environment.yml index 0375f1107d8..c3c4371eadf 100644 --- a/modules/nf-core/verifybamid/verifybamid2/environment.yml +++ b/modules/nf-core/verifybamid/verifybamid2/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vg/construct/environment.yml b/modules/nf-core/vg/construct/environment.yml index 502b6f7effd..27512b7d11a 100644 --- a/modules/nf-core/vg/construct/environment.yml +++ b/modules/nf-core/vg/construct/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vg/deconstruct/environment.yml b/modules/nf-core/vg/deconstruct/environment.yml index 58a7728b0cd..d848baba9ae 100644 --- a/modules/nf-core/vg/deconstruct/environment.yml +++ b/modules/nf-core/vg/deconstruct/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vg/index/environment.yml b/modules/nf-core/vg/index/environment.yml index 502b6f7effd..27512b7d11a 100644 --- a/modules/nf-core/vg/index/environment.yml +++ b/modules/nf-core/vg/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/viennarna/rnacofold/environment.yml b/modules/nf-core/viennarna/rnacofold/environment.yml index 757186a7076..94fbd7652f5 100644 --- a/modules/nf-core/viennarna/rnacofold/environment.yml +++ b/modules/nf-core/viennarna/rnacofold/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::viennarna=2.6.4" + - bioconda::viennarna=2.6.4 diff --git a/modules/nf-core/viennarna/rnafold/environment.yml b/modules/nf-core/viennarna/rnafold/environment.yml index eb62ef69af8..94fbd7652f5 100644 --- a/modules/nf-core/viennarna/rnafold/environment.yml +++ b/modules/nf-core/viennarna/rnafold/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::viennarna=2.6.4" + - bioconda::viennarna=2.6.4 diff --git a/modules/nf-core/viennarna/rnalfold/environment.yml b/modules/nf-core/viennarna/rnalfold/environment.yml index 757186a7076..94fbd7652f5 100644 --- a/modules/nf-core/viennarna/rnalfold/environment.yml +++ b/modules/nf-core/viennarna/rnalfold/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::viennarna=2.6.4" + - bioconda::viennarna=2.6.4 diff --git a/modules/nf-core/vireo/environment.yml b/modules/nf-core/vireo/environment.yml index cc87fb82999..7a537ff7373 100644 --- a/modules/nf-core/vireo/environment.yml +++ b/modules/nf-core/vireo/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::vireosnp=0.5.8" + - bioconda::vireosnp=0.5.8 diff --git a/modules/nf-core/vrhyme/extractunbinned/environment.yml b/modules/nf-core/vrhyme/extractunbinned/environment.yml index 4908e2bce3d..46658ff97b5 100644 --- a/modules/nf-core/vrhyme/extractunbinned/environment.yml +++ b/modules/nf-core/vrhyme/extractunbinned/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vrhyme/linkbins/environment.yml b/modules/nf-core/vrhyme/linkbins/environment.yml index 4908e2bce3d..46658ff97b5 100644 --- a/modules/nf-core/vrhyme/linkbins/environment.yml +++ b/modules/nf-core/vrhyme/linkbins/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vrhyme/vrhyme/environment.yml b/modules/nf-core/vrhyme/vrhyme/environment.yml index b4f66fea212..bc6ae1d2342 100644 --- a/modules/nf-core/vrhyme/vrhyme/environment.yml +++ b/modules/nf-core/vrhyme/vrhyme/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vsearch/cluster/environment.yml b/modules/nf-core/vsearch/cluster/environment.yml index e9b4c9dc6a1..bd00d3552e9 100644 --- a/modules/nf-core/vsearch/cluster/environment.yml +++ b/modules/nf-core/vsearch/cluster/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vsearch/dereplicate/environment.yml b/modules/nf-core/vsearch/dereplicate/environment.yml index 534299a8eae..25dff6b8d14 100644 --- a/modules/nf-core/vsearch/dereplicate/environment.yml +++ b/modules/nf-core/vsearch/dereplicate/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::vsearch=2.28.1" + - bioconda::vsearch=2.28.1 diff --git a/modules/nf-core/vsearch/fastqfilter/environment.yml b/modules/nf-core/vsearch/fastqfilter/environment.yml index 534299a8eae..25dff6b8d14 100644 --- a/modules/nf-core/vsearch/fastqfilter/environment.yml +++ b/modules/nf-core/vsearch/fastqfilter/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::vsearch=2.28.1" + - bioconda::vsearch=2.28.1 diff --git a/modules/nf-core/vsearch/sintax/environment.yml b/modules/nf-core/vsearch/sintax/environment.yml index acba2f679e8..817588c42fb 100644 --- a/modules/nf-core/vsearch/sintax/environment.yml +++ b/modules/nf-core/vsearch/sintax/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vsearch/sort/environment.yml b/modules/nf-core/vsearch/sort/environment.yml index acba2f679e8..817588c42fb 100644 --- a/modules/nf-core/vsearch/sort/environment.yml +++ b/modules/nf-core/vsearch/sort/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vsearch/usearchglobal/environment.yml b/modules/nf-core/vsearch/usearchglobal/environment.yml index acba2f679e8..817588c42fb 100644 --- a/modules/nf-core/vsearch/usearchglobal/environment.yml +++ b/modules/nf-core/vsearch/usearchglobal/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vt/decompose/environment.yml b/modules/nf-core/vt/decompose/environment.yml index 36139fa76a9..c5d350af4d5 100644 --- a/modules/nf-core/vt/decompose/environment.yml +++ b/modules/nf-core/vt/decompose/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/vt/decomposeblocksub/environment.yml b/modules/nf-core/vt/decomposeblocksub/environment.yml index 3f2cbb9b9e1..c5d350af4d5 100644 --- a/modules/nf-core/vt/decomposeblocksub/environment.yml +++ b/modules/nf-core/vt/decomposeblocksub/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::vt=2015.11.10" + - bioconda::vt=2015.11.10 diff --git a/modules/nf-core/vt/decomposeblocksub/meta.yml b/modules/nf-core/vt/decomposeblocksub/meta.yml index 39d67b84ebb..dd6924a5e93 100644 --- a/modules/nf-core/vt/decomposeblocksub/meta.yml +++ b/modules/nf-core/vt/decomposeblocksub/meta.yml @@ -51,7 +51,7 @@ output: description: The decomposed VCF file pattern: "*.vcf.gz" ontologies: - - edam: "http://edamontology.org/format_3016" + - edam: "http://edamontology.org/format_3016" - versions: - versions.yml: type: file diff --git a/modules/nf-core/vt/normalize/environment.yml b/modules/nf-core/vt/normalize/environment.yml index 36139fa76a9..c5d350af4d5 100644 --- a/modules/nf-core/vt/normalize/environment.yml +++ b/modules/nf-core/vt/normalize/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml index 7981870f204..2fe6b929af6 100644 --- a/modules/nf-core/wfmash/environment.yml +++ b/modules/nf-core/wfmash/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wgsim/environment.yml b/modules/nf-core/wgsim/environment.yml index 5ca5c63a6dc..0f457b29cbf 100644 --- a/modules/nf-core/wgsim/environment.yml +++ b/modules/nf-core/wgsim/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/whamg/environment.yml b/modules/nf-core/whamg/environment.yml index cedbc531078..88bc2d0fb64 100644 --- a/modules/nf-core/whamg/environment.yml +++ b/modules/nf-core/whamg/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/windowmasker/convert/environment.yml b/modules/nf-core/windowmasker/convert/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/windowmasker/convert/environment.yml +++ b/modules/nf-core/windowmasker/convert/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/windowmasker/mkcounts/environment.yml b/modules/nf-core/windowmasker/mkcounts/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/windowmasker/mkcounts/environment.yml +++ b/modules/nf-core/windowmasker/mkcounts/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/windowmasker/ustat/environment.yml b/modules/nf-core/windowmasker/ustat/environment.yml index 777e097ed75..968930b63d9 100644 --- a/modules/nf-core/windowmasker/ustat/environment.yml +++ b/modules/nf-core/windowmasker/ustat/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wipertools/fastqgather/environment.yml b/modules/nf-core/wipertools/fastqgather/environment.yml index 711f32a1873..968eb0288e8 100644 --- a/modules/nf-core/wipertools/fastqgather/environment.yml +++ b/modules/nf-core/wipertools/fastqgather/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::wipertools=1.1.4" + - bioconda::wipertools=1.1.4 diff --git a/modules/nf-core/wipertools/fastqgather/main.nf b/modules/nf-core/wipertools/fastqgather/main.nf index 1eac317a8a7..cab21ffd3fa 100644 --- a/modules/nf-core/wipertools/fastqgather/main.nf +++ b/modules/nf-core/wipertools/fastqgather/main.nf @@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQGATHER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0': - 'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/wipertools:1.1.5--pyhdfd78af_0': + 'biocontainers/wipertools:1.1.5--pyhdfd78af_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap index 8862a9774ed..bcc555c02ef 100644 --- a/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap +++ b/modules/nf-core/wipertools/fastqgather/tests/main.nf.test.snap @@ -28,9 +28,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.2" }, - "timestamp": "2025-01-18T07:48:36.495342" + "timestamp": "2025-01-31T10:49:02.021919993" }, "merge two gzipped fastq - fastq.gz": { "content": [ @@ -61,8 +61,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.2" }, - "timestamp": "2025-01-18T07:48:25.182554" + "timestamp": "2025-01-31T10:48:43.687455488" } -} \ No newline at end of file +} diff --git a/modules/nf-core/wipertools/fastqscatter/environment.yml b/modules/nf-core/wipertools/fastqscatter/environment.yml index 711f32a1873..968eb0288e8 100644 --- a/modules/nf-core/wipertools/fastqscatter/environment.yml +++ b/modules/nf-core/wipertools/fastqscatter/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::wipertools=1.1.4" + - bioconda::wipertools=1.1.4 diff --git a/modules/nf-core/wipertools/fastqscatter/main.nf b/modules/nf-core/wipertools/fastqscatter/main.nf index fdac3f90636..a83a775da34 100644 --- a/modules/nf-core/wipertools/fastqscatter/main.nf +++ b/modules/nf-core/wipertools/fastqscatter/main.nf @@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQSCATTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0': - 'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/wipertools:1.1.5--pyhdfd78af_0': + 'biocontainers/wipertools:1.1.5--pyhdfd78af_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap index ef7b51e83bb..de73ca51813 100644 --- a/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap +++ b/modules/nf-core/wipertools/fastqscatter/tests/main.nf.test.snap @@ -34,9 +34,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.2" }, - "timestamp": "2025-01-18T17:33:01.715401" + "timestamp": "2025-01-31T10:49:30.871539752" }, "test1 - fastq": { "content": [ @@ -73,8 +73,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.2" }, - "timestamp": "2025-01-18T17:32:49.482796" + "timestamp": "2025-01-31T10:49:16.633370109" } } \ No newline at end of file diff --git a/modules/nf-core/wipertools/fastqwiper/environment.yml b/modules/nf-core/wipertools/fastqwiper/environment.yml index 711f32a1873..968eb0288e8 100644 --- a/modules/nf-core/wipertools/fastqwiper/environment.yml +++ b/modules/nf-core/wipertools/fastqwiper/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::wipertools=1.1.4" + - bioconda::wipertools=1.1.4 diff --git a/modules/nf-core/wipertools/fastqwiper/main.nf b/modules/nf-core/wipertools/fastqwiper/main.nf index 3e7f24362e2..cab3373df24 100644 --- a/modules/nf-core/wipertools/fastqwiper/main.nf +++ b/modules/nf-core/wipertools/fastqwiper/main.nf @@ -4,8 +4,8 @@ process WIPERTOOLS_FASTQWIPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0': - 'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/wipertools:1.1.5--pyhdfd78af_0': + 'biocontainers/wipertools:1.1.5--pyhdfd78af_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap b/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap index dc928138372..cdc972039cf 100644 --- a/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap +++ b/modules/nf-core/wipertools/fastqwiper/tests/main.nf.test.snap @@ -97,4 +97,4 @@ }, "timestamp": "2025-01-18T07:49:09.920936" } -} \ No newline at end of file +} diff --git a/modules/nf-core/wipertools/reportgather/environment.yml b/modules/nf-core/wipertools/reportgather/environment.yml index 711f32a1873..968eb0288e8 100644 --- a/modules/nf-core/wipertools/reportgather/environment.yml +++ b/modules/nf-core/wipertools/reportgather/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::wipertools=1.1.4" + - bioconda::wipertools=1.1.4 diff --git a/modules/nf-core/wipertools/reportgather/main.nf b/modules/nf-core/wipertools/reportgather/main.nf index 045e271bd9f..3a0b81b441f 100644 --- a/modules/nf-core/wipertools/reportgather/main.nf +++ b/modules/nf-core/wipertools/reportgather/main.nf @@ -4,8 +4,8 @@ process WIPERTOOLS_REPORTGATHER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wipertools:1.1.4--pyhdfd78af_0': - 'biocontainers/wipertools:1.1.4--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/wipertools:1.1.5--pyhdfd78af_0': + 'biocontainers/wipertools:1.1.5--pyhdfd78af_0' }" input: tuple val(meta), path(report) diff --git a/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap b/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap index 8b314eab577..c0c91b96c3c 100644 --- a/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap +++ b/modules/nf-core/wipertools/reportgather/tests/main.nf.test.snap @@ -93,4 +93,4 @@ }, "timestamp": "2025-01-18T07:49:32.055316" } -} \ No newline at end of file +} diff --git a/modules/nf-core/wisecondorx/convert/environment.yml b/modules/nf-core/wisecondorx/convert/environment.yml index 90e62a7c494..b6bd671b7d6 100644 --- a/modules/nf-core/wisecondorx/convert/environment.yml +++ b/modules/nf-core/wisecondorx/convert/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wisecondorx/gender/environment.yml b/modules/nf-core/wisecondorx/gender/environment.yml index 90e62a7c494..b6bd671b7d6 100644 --- a/modules/nf-core/wisecondorx/gender/environment.yml +++ b/modules/nf-core/wisecondorx/gender/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wisecondorx/newref/environment.yml b/modules/nf-core/wisecondorx/newref/environment.yml index 90e62a7c494..b6bd671b7d6 100644 --- a/modules/nf-core/wisecondorx/newref/environment.yml +++ b/modules/nf-core/wisecondorx/newref/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/wisecondorx/predict/environment.yml b/modules/nf-core/wisecondorx/predict/environment.yml index 90e62a7c494..b6bd671b7d6 100644 --- a/modules/nf-core/wisecondorx/predict/environment.yml +++ b/modules/nf-core/wisecondorx/predict/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/xengsort/index/environment.yml b/modules/nf-core/xengsort/index/environment.yml index 43a6ecdce0b..e566a9bc5f9 100644 --- a/modules/nf-core/xengsort/index/environment.yml +++ b/modules/nf-core/xengsort/index/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::xengsort=2.0.5" + - bioconda::xengsort=2.0.5 diff --git a/modules/nf-core/xz/compress/environment.yml b/modules/nf-core/xz/compress/environment.yml index 240428da6af..3bc864f762a 100644 --- a/modules/nf-core/xz/compress/environment.yml +++ b/modules/nf-core/xz/compress/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "xz=5.2.6" + - xz=5.2.6 diff --git a/modules/nf-core/xz/decompress/environment.yml b/modules/nf-core/xz/decompress/environment.yml index 240428da6af..3bc864f762a 100644 --- a/modules/nf-core/xz/decompress/environment.yml +++ b/modules/nf-core/xz/decompress/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "xz=5.2.6" + - xz=5.2.6 diff --git a/modules/nf-core/yahs/environment.yml b/modules/nf-core/yahs/environment.yml index cb2acec87ed..02d7996b714 100644 --- a/modules/nf-core/yahs/environment.yml +++ b/modules/nf-core/yahs/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/yak/count/environment.yml b/modules/nf-core/yak/count/environment.yml index 907edbb62f6..95cf97d5c64 100644 --- a/modules/nf-core/yak/count/environment.yml +++ b/modules/nf-core/yak/count/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::yak=0.1" + - bioconda::yak=0.1 diff --git a/modules/nf-core/yara/index/environment.yml b/modules/nf-core/yara/index/environment.yml index 90714436ab0..b80b4cb82bf 100644 --- a/modules/nf-core/yara/index/environment.yml +++ b/modules/nf-core/yara/index/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/yara/mapper/environment.yml b/modules/nf-core/yara/mapper/environment.yml index 5daa8992144..6846439818b 100644 --- a/modules/nf-core/yara/mapper/environment.yml +++ b/modules/nf-core/yara/mapper/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/zip/environment.yml b/modules/nf-core/zip/environment.yml index e93c649f443..2461589539a 100644 --- a/modules/nf-core/zip/environment.yml +++ b/modules/nf-core/zip/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/yaml-schema.json b/modules/yaml-schema.json deleted file mode 120000 index d84030e9dc3..00000000000 --- a/modules/yaml-schema.json +++ /dev/null @@ -1 +0,0 @@ -meta-schema.json \ No newline at end of file diff --git a/modules/yaml-schema.json b/modules/yaml-schema.json new file mode 100644 index 00000000000..d84030e9dc3 --- /dev/null +++ b/modules/yaml-schema.json @@ -0,0 +1 @@ +meta-schema.json \ No newline at end of file diff --git a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test index b8e9da9abda..d90c9d49cdb 100644 --- a/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test +++ b/subworkflows/nf-core/bam_dedup_umi/tests/main.nf.test @@ -8,9 +8,9 @@ nextflow_workflow { tag "subworkflows" tag "subworkflows_nfcore" tag "subworkflows/bam_dedup_umi" - tag "bam_dedup_stats_samtools_umicollapse" - tag "bam_dedup_stats_samtools_umitools" - tag "bam_sort_stats_samtools" + tag "subworkflows/bam_dedup_stats_samtools_umicollapse" + tag "subworkflows/bam_dedup_stats_samtools_umitools" + tag "subworkflows/bam_sort_stats_samtools" tag "umitools/prepareforrsem" tag "samtools/sort" @@ -96,4 +96,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/differential_functional_enrichment/meta.yml b/subworkflows/nf-core/differential_functional_enrichment/meta.yml index e296e3fe54e..aa97cb914b1 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/meta.yml +++ b/subworkflows/nf-core/differential_functional_enrichment/meta.yml @@ -9,6 +9,9 @@ components: - gprofiler2/gost - gsea/gsea - propr/grea + - custom/tabulartogseagct + - custom/tabulartogseacls + - custom/tabulartogseachip input: - ch_input: description: Channel with the input data for functional analysis. @@ -133,7 +136,7 @@ output: pattern: "*gsea_report_for_${target}.tsv" - grea_results: description: | - Channel containing the output from GREA. + Channel containing the output from GREA. structure: - meta: type: map diff --git a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test index e1138d4f79e..bb01beb8e80 100644 --- a/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test +++ b/subworkflows/nf-core/differential_functional_enrichment/tests/main.nf.test @@ -13,6 +13,10 @@ nextflow_workflow { tag "gsea/gsea" tag "propr" tag "propr/grea" + tag "custom" + tag "custom/tabulartogseagct" + tag "custom/tabulartogseacls" + tag "custom/tabulartogseachip" test("test gprofiler2 - mouse") { tag 'gprofiler2_basic' diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml index 4cf6a0096fc..d9a5be020d4 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml @@ -13,6 +13,7 @@ components: - samtools/index - cat - cat/fastq + - fq/lint - sortmerna - fastq_subsample_fq_salmon - fastq_fastqc_umitools_trimgalore diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test index c5fc4aec98d..e6f3cb33f5b 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_workflow { tag "cat" tag "cat/fastq" tag "fastqc" + tag "fq/lint" tag "sortmerna" tag "subworkflows/fastq_fastqc_umitools_trimgalore" tag "subworkflows/fastq_fastqc_umitools_fastp" diff --git a/subworkflows/nf-core/utils_references/README.md b/subworkflows/nf-core/utils_references/README.md new file mode 100644 index 00000000000..03da289f335 --- /dev/null +++ b/subworkflows/nf-core/utils_references/README.md @@ -0,0 +1,13 @@ +# Disclaimer + +This `utils_references/` folder contains for now two functions and a schema. +This is really meant for a POC and should not be installed by anyone except @maxulysse. +But that was the easiest way to share functions and a schema between three different pipelines and still showcase the logic. +This might evolve in the future, possibly towards a proper plugin. + +If you do so, please be aware that: + +- @maxulysse has hacked the `main.nf` to test the functions and the schema +- This is really meant to evolve in the future and can be deleted at any moment without prior notice. + +That being said, if you still want to use it or want to know more about it, please check the `#references` channel on the nf-core slack. diff --git a/subworkflows/nf-core/utils_references/main.nf b/subworkflows/nf-core/utils_references/main.nf new file mode 100644 index 00000000000..c557acc0a6e --- /dev/null +++ b/subworkflows/nf-core/utils_references/main.nf @@ -0,0 +1,60 @@ +// DISCLAIMER: +// This subworkflow is just to test the functions and the schema +// It should not be used in any pipeline + +// This include statement can also be deleted +include { samplesheetToList } from 'plugin/nf-schema' + +workflow UTILS_REFERENCES { + take: + yaml_reference + param_file + param_value + attribute_file + attribute_value + basepath + + main: + references = Channel.fromList(samplesheetToList(yaml_reference, "${projectDir}/subworkflows/nf-core/utils_references/schema_references.json")) + + // GIVING up writing a test for the functions, so writing a subworkflow to test it + references_file = get_references_file(references, param_file, attribute_file, basepath) + references_value = get_references_value(references, param_value, attribute_value) + + emit: + references_file + references_value +} +// You can delete everything before this line (including this line) + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS TO EXTRACT REFERENCES FILES OR VALUES FROM THE REFERENCES YAML OR PARAMS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +def get_references_file(references, param, attribute, basepath) { + return references + .map { meta, _readme -> + if (param || meta[attribute]) { + [meta.subMap(['id']), file(param ?: meta[attribute].replace('${params.igenomes_base}', basepath), checkIfExists: true)] + } + else { + null + } + } + .collect() +} + +def get_references_value(references, param, attribute) { + return references + .map { meta, _readme -> + if (param || meta[attribute]) { + [meta.subMap(['id']), param ?: meta[attribute]] + } + else { + null + } + } + .collect() +} diff --git a/subworkflows/nf-core/utils_references/meta.yml b/subworkflows/nf-core/utils_references/meta.yml new file mode 100644 index 00000000000..491c79c969e --- /dev/null +++ b/subworkflows/nf-core/utils_references/meta.yml @@ -0,0 +1,14 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_references" +description: Functionality for dealing with references that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - references +components: [] +input: [] +output: [] +authors: + - "@maxulysse" +maintainers: + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_references/schema_references.json b/subworkflows/nf-core/utils_references/schema_references.json new file mode 100644 index 00000000000..56829a1086b --- /dev/null +++ b/subworkflows/nf-core/utils_references/schema_references.json @@ -0,0 +1,376 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/nf-core/references/master/assets/schema_asset.json", + "title": "nf-core/references pipeline - params.asset schema", + "description": "Schema for the file provided with params.asset", + "type": "array", + "items": { + "type": "object", + "properties": { + "genome": { + "meta": ["genome", "id"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Genome name must be provided, cannot contain spaces" + }, + "site": { + "meta": ["site"], + "type": "string", + "pattern": "^\\S+$", + "default": "unknown", + "errorMessage": "Website of origin of the reference, cannot contain spaces" + }, + "source": { + "meta": ["source"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Source of genome must be provided, cannot contain spaces" + }, + "source_version": { + "meta": ["source_version"], + "type": "string", + "pattern": "^\\S+$", + "default": "unknown", + "errorMessage": "Source version used to create annotation files (gff/gtf related files), cannot contain spaces" + }, + "species": { + "meta": ["species"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Species of the reference, cannot contain spaces" + }, + "ascat_alleles": { + "meta": ["ascat_alleles"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "ascat_loci": { + "meta": ["ascat_loci"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "ascat_loci_gc": { + "meta": ["ascat_loci_gc"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "bed12": { + "meta": ["bed12"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "bowtie1_index": { + "meta": ["bowtie1_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "Bowtie1 index, cannot contain spaces" + }, + "bowtie2_index": { + "meta": ["bowtie2_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "Bowtie2 index, cannot contain spaces" + }, + "bwamem1_index": { + "meta": ["bwamem1_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "BWA-MEM index, cannot contain spaces" + }, + "bwamem2_index": { + "meta": ["bwamem2_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "BWA-MEM2 index, cannot contain spaces" + }, + "dragmap_hashtable": { + "meta": ["dragmap_hashtable"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "DRAGMAP hashtable, cannot contain spaces" + }, + "chr_dir": { + "meta": ["chr_dir"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "fasta": { + "meta": ["fasta"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.f(ast|n)?a(\\.gz)?$", + "errorMessage": "Fasta file [required when creating a reference], cannot contain spaces" + }, + "fasta_dict": { + "meta": ["fasta_dict"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.dict(\\.gz)?$", + "errorMessage": "Fasta dictionary, cannot contain spaces" + }, + "fasta_fai": { + "meta": ["fasta_fai"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.f(ast|n)?a\\.fai(\\.gz)?$", + "errorMessage": "Fasta index, cannot contain spaces" + }, + "fasta_sizes": { + "meta": ["fasta_sizes"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.f(ast|n)?a\\.sizes(\\.gz)?$", + "errorMessage": "Fasta sizes, cannot contain spaces" + }, + "gff": { + "meta": ["gff"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.gff(\\.gz)?$", + "errorMessage": "GFF3 file, required when no GTF is provided and wanting to build a reference needing such genes annotation, cannot contain spaces" + }, + "gtf": { + "meta": ["gtf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.gtf(\\.gz)?$", + "errorMessage": "GTF file, required when no GFF3 is provided and wanting to build a reference needing such genes annotation, cannot contain spaces" + }, + "hisat2_index": { + "meta": ["hisat2_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "HISAT2 index, cannot contain spaces" + }, + "intervals_bed": { + "meta": ["intervals_bed"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.bed$", + "errorMessage": "Fasta intervals bed, cannot contain spaces " + }, + "kallisto_index": { + "meta": ["kallisto_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "Kallisto index, cannot contain spaces" + }, + "macs_gsize": { + "meta": ["macs_gsize"], + "type": "number", + "errorMessage": "TODO" + }, + "mito_name": { + "meta": ["mito_name"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "TODO" + }, + "msisensorpro_list": { + "meta": ["msisensorpro_list"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "MSIsensor-pro list, cannot contain spaces" + }, + "ngscheckmate_bed": { + "meta": ["ngscheckmate_bed"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.bed$", + "errorMessage": "ngscheckmate bed, cannot contain spaces " + }, + "readme": { + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "README file describing the reference, cannot contain spaces" + }, + "rsem_index": { + "meta": ["rsem_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "RSEM index, cannot contain spaces" + }, + "salmon_index": { + "meta": ["salmon_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "Salmon index, cannot contain spaces" + }, + "splice_sites": { + "meta": ["splice_sites"], + "type": "string", + "format": "path", + "pattern": "^\\S+(\\.splice_sites)(\\.txt)?$", + "errorMessage": "Splice sites [can be generated with HISAT2], cannot contain spaces" + }, + "star_index": { + "meta": ["star_index"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "STAR index, cannot contain spaces" + }, + "snpeff_db": { + "meta": ["snpeff_db"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "SnpEff database, cannot contain spaces" + }, + "transcript_fasta": { + "meta": ["transcript_fasta"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.f(ast|n)?a(\\.gz)?$", + "errorMessage": "Transcript fasta [can be generated with RSEM], cannot contain spaces" + }, + "vep_cache_version": { + "meta": ["vep_cache_version"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "VEP cache version, cannot contain spaces" + }, + "vep_genome": { + "meta": ["vep_genome"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "VEP genome, cannot contain spaces" + }, + "vep_species": { + "meta": ["vep_species"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "VEP species, cannot contain spaces" + }, + "vcf_dbsnp_vcf": { + "meta": ["vcf_dbsnp_vcf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "errorMessage": "VCF file (can be bgzipped), cannot contain spaces" + }, + "vcf_dbsnp_vcf_tbi": { + "meta": ["vcf_dbsnp_vcf_tbi"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf\\.gz\\.tbi?$", + "errorMessage": "VCF tabix index, cannot contain spaces" + }, + "vcf_dbsnp_vcf_vqsr": { + "meta": ["vcf_dbsnp_vcf_vqsr"], + "type": "string", + "errorMessage": "VCF VQSR input, can contain spaces" + }, + "vcf_dbsnp_vcf_source": { + "meta": ["vcf_dbsnp_vcf_source"], + "type": "string", + "format": "path", + "pattern": "^\\S+$", + "errorMessage": "Source of dbsnp, cannot contain spaces" + }, + "vcf_germline_resource_vcf": { + "meta": ["vcf_germline_resource_vcf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "errorMessage": "VCF file (can be bgzipped), cannot contain spaces" + }, + "vcf_germline_resource_vcf_tbi": { + "meta": ["vcf_germline_resource_vcf_tbi"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf\\.gz\\.tbi?$", + "errorMessage": "VCF tabix index, cannot contain spaces" + }, + "vcf_germline_resource_vcf_source": { + "meta": ["vcf_germline_resource_vcf_source"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Source of germline_resource, cannot contain spaces" + }, + "vcf_known_indels_vcf": { + "meta": ["vcf_known_indels_vcf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "errorMessage": "VCF file (can be bgzipped), cannot contain spaces" + }, + "vcf_known_indels_vcf_tbi": { + "meta": ["vcf_known_indels_vcf_tbi"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf\\.gz\\.tbi?$", + "errorMessage": "VCF tabix index, cannot contain spaces" + }, + "vcf_known_indels_vcf_source": { + "meta": ["vcf_known_indels_vcf_source"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Source of known_indels, cannot contain spaces" + }, + "vcf_known_snps_vcf": { + "meta": ["vcf_known_snps_vcf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "errorMessage": "VCF file (can be bgzipped), cannot contain spaces" + }, + "vcf_known_snps_vcf_tbi": { + "meta": ["vcf_known_snps_vcf_tbi"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf\\.gz\\.tbi?$", + "errorMessage": "VCF tabix index, cannot contain spaces" + }, + "vcf_known_snps_vcf_source": { + "meta": ["vcf_known_snps_vcf_source"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Source of known_snps, cannot contain spaces" + }, + "vcf_pon_vcf": { + "meta": ["vcf_pon_vcf"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "errorMessage": "VCF file (can be bgzipped), cannot contain spaces" + }, + "vcf_pon_vcf_tbi": { + "meta": ["vcf_pon_vcf_tbi"], + "type": "string", + "format": "path", + "pattern": "^\\S+\\.vcf\\.gz\\.tbi?$", + "errorMessage": "VCF tabix index, cannot contain spaces" + }, + "vcf_pon_vcf_source": { + "meta": ["vcf_pon_vcf_source"], + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Source of pon, cannot contain spaces" + } + }, + "required": ["genome"] + } +} diff --git a/subworkflows/nf-core/utils_references/tests/main.nf.test b/subworkflows/nf-core/utils_references/tests/main.nf.test new file mode 100644 index 00000000000..d16de16e686 --- /dev/null +++ b/subworkflows/nf-core/utils_references/tests/main.nf.test @@ -0,0 +1,27 @@ +nextflow_workflow { + + name "Test Workflow UTILS_REFERENCES" + script "../main.nf" + workflow "UTILS_REFERENCES" + + test("references_file with params - references_value without params") { + + when { + workflow { + """ + input[0] = 'https://raw.githubusercontent.com/nf-core/references-assets/main/genomes/Homo_sapiens/test/GRCh38_chr22.yml' + input[1] = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' + input[2] = null + input[3] = 'fasta' + input[4] = 'species' + input[5] = 'https://raw.githubusercontent.com/nf-core/' + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + } +} diff --git a/subworkflows/nf-core/utils_references/tests/main.nf.test.snap b/subworkflows/nf-core/utils_references/tests/main.nf.test.snap new file mode 100644 index 00000000000..f5bf3bb34ba --- /dev/null +++ b/subworkflows/nf-core/utils_references/tests/main.nf.test.snap @@ -0,0 +1,45 @@ +{ + "references_file with params - references_value without params": { + "content": [ + { + "0": [ + [ + { + "id": "GRCh38_chr22" + }, + "/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + ] + ], + "1": [ + [ + { + "id": "GRCh38_chr22" + }, + "Homo_sapiens" + ] + ], + "references_file": [ + [ + { + "id": "GRCh38_chr22" + }, + "/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + ] + ], + "references_value": [ + [ + { + "id": "GRCh38_chr22" + }, + "Homo_sapiens" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-03T18:21:58.076068554" + } +} \ No newline at end of file diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 2ffaa77c9f4..104b8ec0a33 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -710,6 +710,14 @@ params { taxa_sqlite_traverse_pkl = "${params.test_data_base}/data/genomics/prokaryotes/metagenome/taxonomy/misc/taxa_sqlite_traverse.pkl" } } + 'streptococcus_agalactiae' { + 'genome' { + emu_db = "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/genome/emu" + } + 'nanopore' { + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/streptococcus_agalactiae/nanopore/fastq/test.fastq.gz" + } + } 'saccharomyces_cerevisiae' { 'genome' { samplesheet = "${params.test_data_base}/data/genomics/eukaryotes/saccharomyces_cerevisiae/samplesheet.csv"