Merge branch 'master' into sylph_tax

.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

.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)])

.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 ./

.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:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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