From a8f4b2bacd5a25f6b7d85c998c99bfce32f30f1a Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 1 Feb 2024 15:12:03 +0100 Subject: [PATCH 1/3] update modules --- modules.json | 30 +-- modules/nf-core/fastqc/main.nf | 55 ----- modules/nf-core/fastqc/meta.yml | 57 ----- modules/nf-core/fastqc/tests/main.nf.test | 212 ------------------ .../nf-core/fastqc/tests/main.nf.test.snap | 20 -- modules/nf-core/fastqc/tests/tags.yml | 2 - modules/nf-core/gfaffix/environment.yml | 7 + modules/nf-core/gfaffix/main.nf | 2 +- modules/nf-core/gfaffix/meta.yml | 3 +- modules/nf-core/odgi/build/environment.yml | 7 + modules/nf-core/odgi/build/main.nf | 6 +- modules/nf-core/odgi/build/meta.yml | 7 +- modules/nf-core/odgi/build/tests/main.nf.test | 34 +++ .../odgi/build/tests/main.nf.test.snap | 33 +++ .../{fastqc => odgi/draw}/environment.yml | 4 +- modules/nf-core/odgi/draw/main.nf | 6 +- modules/nf-core/odgi/draw/meta.yml | 7 +- modules/nf-core/odgi/draw/test/main.nf.test | 35 +++ .../nf-core/odgi/draw/test/main.nf.test.snap | 33 +++ modules/nf-core/odgi/layout/environment.yml | 7 + modules/nf-core/odgi/layout/main.nf | 6 +- modules/nf-core/odgi/layout/meta.yml | 7 +- .../nf-core/odgi/layout/tests/main.nf.test | 35 +++ .../odgi/layout/tests/main.nf.test.snap | 51 +++++ .../nf-core/odgi/layout/tests/nextflow.config | 7 + modules/nf-core/odgi/sort/environment.yml | 7 + modules/nf-core/odgi/sort/main.nf | 6 +- modules/nf-core/odgi/sort/meta.yml | 7 +- modules/nf-core/odgi/sort/tests/main.nf.test | 34 +++ .../nf-core/odgi/sort/tests/main.nf.test.snap | 33 +++ modules/nf-core/odgi/squeeze/environment.yml | 7 + modules/nf-core/odgi/squeeze/main.nf | 6 +- modules/nf-core/odgi/squeeze/meta.yml | 7 +- .../nf-core/odgi/squeeze/tests/main.nf.test | 34 +++ .../odgi/squeeze/tests/main.nf.test.snap | 33 +++ modules/nf-core/odgi/stats/environment.yml | 7 + modules/nf-core/odgi/stats/main.nf | 6 +- modules/nf-core/odgi/stats/meta.yml | 7 +- modules/nf-core/odgi/stats/tests/main.nf.test | 34 +++ .../odgi/stats/tests/main.nf.test.snap | 39 ++++ modules/nf-core/odgi/unchop/environment.yml | 7 + modules/nf-core/odgi/unchop/main.nf | 6 +- modules/nf-core/odgi/unchop/meta.yml | 7 +- .../nf-core/odgi/unchop/tests/main.nf.test | 34 +++ .../odgi/unchop/tests/main.nf.test.snap | 33 +++ modules/nf-core/odgi/view/environment.yml | 7 + modules/nf-core/odgi/view/main.nf | 6 +- modules/nf-core/odgi/view/meta.yml | 7 +- modules/nf-core/odgi/view/tests/main.nf.test | 34 +++ .../nf-core/odgi/view/tests/main.nf.test.snap | 33 +++ modules/nf-core/odgi/viz/environment.yml | 7 + modules/nf-core/odgi/viz/main.nf | 6 +- modules/nf-core/odgi/viz/meta.yml | 7 +- modules/nf-core/odgi/viz/tests/main.nf.test | 34 +++ .../nf-core/odgi/viz/tests/main.nf.test.snap | 33 +++ .../nf-core/samtools/faidx/environment.yml | 8 + modules/nf-core/samtools/faidx/main.nf | 6 +- modules/nf-core/samtools/faidx/meta.yml | 4 + .../nf-core/seqwish/induce/environment.yml | 7 + modules/nf-core/seqwish/induce/main.nf | 2 +- modules/nf-core/seqwish/induce/meta.yml | 3 +- modules/nf-core/smoothxg/environment.yml | 7 + modules/nf-core/smoothxg/main.nf | 6 +- modules/nf-core/smoothxg/meta.yml | 3 +- modules/nf-core/smoothxg/tests/main.nf.test | 56 +++++ .../nf-core/smoothxg/tests/main.nf.test.snap | 39 ++++ .../nf-core/smoothxg/tests/nextflow.config | 11 + modules/nf-core/smoothxg/tests/tags.yml | 2 + modules/nf-core/tabix/bgzip/environment.yml | 7 + modules/nf-core/tabix/bgzip/main.nf | 2 +- modules/nf-core/tabix/bgzip/meta.yml | 5 + modules/nf-core/wfmash/environment.yml | 7 + modules/nf-core/wfmash/main.nf | 6 +- modules/nf-core/wfmash/meta.yml | 7 +- modules/nf-core/wfmash/tests/main.nf.test | 39 ++++ .../nf-core/wfmash/tests/main.nf.test.snap | 33 +++ modules/nf-core/wfmash/tests/nextflow.config | 12 + modules/nf-core/wfmash/tests/tags.yml | 2 + 78 files changed, 1030 insertions(+), 445 deletions(-) delete mode 100644 modules/nf-core/fastqc/main.nf delete mode 100644 modules/nf-core/fastqc/meta.yml delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/gfaffix/environment.yml create mode 100644 modules/nf-core/odgi/build/environment.yml create mode 100644 modules/nf-core/odgi/build/tests/main.nf.test create mode 100644 modules/nf-core/odgi/build/tests/main.nf.test.snap rename modules/nf-core/{fastqc => odgi/draw}/environment.yml (61%) create mode 100644 modules/nf-core/odgi/draw/test/main.nf.test create mode 100644 modules/nf-core/odgi/draw/test/main.nf.test.snap create mode 100644 modules/nf-core/odgi/layout/environment.yml create mode 100644 modules/nf-core/odgi/layout/tests/main.nf.test create mode 100644 modules/nf-core/odgi/layout/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/layout/tests/nextflow.config create mode 100644 modules/nf-core/odgi/sort/environment.yml create mode 100644 modules/nf-core/odgi/sort/tests/main.nf.test create mode 100644 modules/nf-core/odgi/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/squeeze/environment.yml create mode 100644 modules/nf-core/odgi/squeeze/tests/main.nf.test create mode 100644 modules/nf-core/odgi/squeeze/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/stats/environment.yml create mode 100644 modules/nf-core/odgi/stats/tests/main.nf.test create mode 100644 modules/nf-core/odgi/stats/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/unchop/environment.yml create mode 100644 modules/nf-core/odgi/unchop/tests/main.nf.test create mode 100644 modules/nf-core/odgi/unchop/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/view/environment.yml create mode 100644 modules/nf-core/odgi/view/tests/main.nf.test create mode 100644 modules/nf-core/odgi/view/tests/main.nf.test.snap create mode 100644 modules/nf-core/odgi/viz/environment.yml create mode 100644 modules/nf-core/odgi/viz/tests/main.nf.test create mode 100644 modules/nf-core/odgi/viz/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/faidx/environment.yml create mode 100644 modules/nf-core/seqwish/induce/environment.yml create mode 100644 modules/nf-core/smoothxg/environment.yml create mode 100644 modules/nf-core/smoothxg/tests/main.nf.test create mode 100644 modules/nf-core/smoothxg/tests/main.nf.test.snap create mode 100644 modules/nf-core/smoothxg/tests/nextflow.config create mode 100644 modules/nf-core/smoothxg/tests/tags.yml create mode 100644 modules/nf-core/tabix/bgzip/environment.yml create mode 100644 modules/nf-core/wfmash/environment.yml create mode 100644 modules/nf-core/wfmash/tests/main.nf.test create mode 100644 modules/nf-core/wfmash/tests/main.nf.test.snap create mode 100644 modules/nf-core/wfmash/tests/nextflow.config create mode 100644 modules/nf-core/wfmash/tests/tags.yml diff --git a/modules.json b/modules.json index 3fed4959..7b0774ba 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "gfaffix": { "branch": "master", - "git_sha": "f1839b597eab2cdcdf05dd8a9419581d76aca197", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { @@ -22,72 +22,72 @@ }, "odgi/build": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/draw": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/layout": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/sort": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/squeeze": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/stats": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/unchop": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/view": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "odgi/viz": { "branch": "master", - "git_sha": "2d8f8fd533fc945358ce11eede8c5e2c86c36e8d", + "git_sha": "a474115d309422f44bdd66e04a0926f3ac6aff47", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["modules"] }, "seqwish/induce": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "smoothxg": { "branch": "master", - "git_sha": "d7c40cb04c94c408608ceabfdc14a443915a87fe", + "git_sha": "bd863b09cc7ef834dd62d5fd687e941cac2daf64", "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "wfmash": { "branch": "master", - "git_sha": "96fadda088c6e79777ba8eef939e36bb03a69c65", + "git_sha": "8cbeaa5063f08952682517597d4e8d6e35bbcd1a", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 9e19a74c..00000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index ee5507e0..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -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 files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 1f21c664..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // 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) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - 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) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // 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), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("versions") } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } - ) - } - } - -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index 5d624bb8..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,20 +0,0 @@ -{ - "sarscov2 single-end [fastq] - stub": { - "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "timestamp": "2024-01-17T18:40:57.254299" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "timestamp": "2024-01-17T18:36:50.033627" - } -} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294b..00000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/gfaffix/environment.yml b/modules/nf-core/gfaffix/environment.yml new file mode 100644 index 00000000..09e63d24 --- /dev/null +++ b/modules/nf-core/gfaffix/environment.yml @@ -0,0 +1,7 @@ +name: gfaffix +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gfaffix=0.1.5 diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index 64f85bc8..561e02d8 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -2,7 +2,7 @@ process GFAFFIX { tag "$meta.id" label 'process_single' - conda "bioconda::gfaffix=0.1.5" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gfaffix:0.1.5--h031d066_0 ' : diff --git a/modules/nf-core/gfaffix/meta.yml b/modules/nf-core/gfaffix/meta.yml index 0c3924a3..384696cf 100644 --- a/modules/nf-core/gfaffix/meta.yml +++ b/modules/nf-core/gfaffix/meta.yml @@ -23,7 +23,6 @@ input: type: file description: Variation graph in GFA format pattern: "*.{gfa}" - output: - meta: type: map @@ -44,3 +43,5 @@ output: pattern: "versions.yml" authors: - "@heuermh" +maintainers: + - "@heuermh" diff --git a/modules/nf-core/odgi/build/environment.yml b/modules/nf-core/odgi/build/environment.yml new file mode 100644 index 00000000..4ae56d26 --- /dev/null +++ b/modules/nf-core/odgi/build/environment.yml @@ -0,0 +1,7 @@ +name: odgi_build +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/build/main.nf b/modules/nf-core/odgi/build/main.nf index 938c16bb..c1bf3402 100644 --- a/modules/nf-core/odgi/build/main.nf +++ b/modules/nf-core/odgi/build/main.nf @@ -2,10 +2,10 @@ process ODGI_BUILD { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/build/meta.yml b/modules/nf-core/odgi/build/meta.yml index f37a95e2..8ec55074 100644 --- a/modules/nf-core/odgi/build/meta.yml +++ b/modules/nf-core/odgi/build/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in GFA v1.0 format pattern: "*.{gfa}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: File containing a pangenome graph in ODGI binary format. Usually ends with '.og' pattern: "*.{og}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/build/tests/main.nf.test b/modules/nf-core/odgi/build/tests/main.nf.test new file mode 100644 index 00000000..5d185c37 --- /dev/null +++ b/modules/nf-core/odgi/build/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_BUILD" + script "../main.nf" + process "ODGI_BUILD" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/build" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, +// { assert snapshot(process.out).match() } // the odgi file on disk may not be deterministic, but the graph itself is + ) + } + + } + +} diff --git a/modules/nf-core/odgi/build/tests/main.nf.test.snap b/modules/nf-core/odgi/build/tests/main.nf.test.snap new file mode 100644 index 00000000..f2254ad0 --- /dev/null +++ b/modules/nf-core/odgi/build/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,8660c0f724a54d7346575ac38ff0b329" + ] + ], + "1": [ + "versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553" + ], + "og": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,8660c0f724a54d7346575ac38ff0b329" + ] + ], + "versions": [ + "versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553" + ] + } + ], + "timestamp": "2024-01-30T11:07:44.462811986" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/odgi/draw/environment.yml similarity index 61% rename from modules/nf-core/fastqc/environment.yml rename to modules/nf-core/odgi/draw/environment.yml index 1787b38a..2424dff6 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/odgi/draw/environment.yml @@ -1,7 +1,7 @@ -name: fastqc +name: odgi_draw channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::fastqc=0.12.1 + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/draw/main.nf b/modules/nf-core/odgi/draw/main.nf index 426c258e..fa1de741 100644 --- a/modules/nf-core/odgi/draw/main.nf +++ b/modules/nf-core/odgi/draw/main.nf @@ -2,10 +2,10 @@ process ODGI_DRAW { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph), path(lay) diff --git a/modules/nf-core/odgi/draw/meta.yml b/modules/nf-core/odgi/draw/meta.yml index 5c32b36b..807463ac 100644 --- a/modules/nf-core/odgi/draw/meta.yml +++ b/modules/nf-core/odgi/draw/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -28,7 +27,6 @@ input: type: file description: 2D layout from 'odgi layout' in LAY binary format pattern: "*.{lay}" - output: - meta: type: map @@ -43,6 +41,7 @@ output: type: file description: File in PNG format containing a 2D drawing of a pangenome graph pattern: "*.{png}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/draw/test/main.nf.test b/modules/nf-core/odgi/draw/test/main.nf.test new file mode 100644 index 00000000..0306ccb8 --- /dev/null +++ b/modules/nf-core/odgi/draw/test/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process ODGI_DRAW" + script "../main.nf" + process "ODGI_DRAW" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/draw" + + test("homo_sapiens - pangenome - odgi - pangenome_og - pangenome_lay") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['odgi']['pangenome_og'], checkIfExists: true), + file(params.test_data['homo_sapiens']['pangenome']['odgi']['pangenome_lay'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/draw/test/main.nf.test.snap b/modules/nf-core/odgi/draw/test/main.nf.test.snap new file mode 100644 index 00000000..f81580f1 --- /dev/null +++ b/modules/nf-core/odgi/draw/test/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - odgi - pangenome_og - pangenome_lay": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.png:md5,2024bc28ff028163094fa1070da028db" + ] + ], + "1": [ + "versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3" + ], + "png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.png:md5,2024bc28ff028163094fa1070da028db" + ] + ], + "versions": [ + "versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3" + ] + } + ], + "timestamp": "2024-01-30T11:03:39.412763234" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/layout/environment.yml b/modules/nf-core/odgi/layout/environment.yml new file mode 100644 index 00000000..82212fc8 --- /dev/null +++ b/modules/nf-core/odgi/layout/environment.yml @@ -0,0 +1,7 @@ +name: odgi_layout +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/layout/main.nf b/modules/nf-core/odgi/layout/main.nf index 22e7c438..27ae4ae0 100644 --- a/modules/nf-core/odgi/layout/main.nf +++ b/modules/nf-core/odgi/layout/main.nf @@ -2,10 +2,10 @@ process ODGI_LAYOUT { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/layout/meta.yml b/modules/nf-core/odgi/layout/meta.yml index 5c65794a..5d7694a3 100644 --- a/modules/nf-core/odgi/layout/meta.yml +++ b/modules/nf-core/odgi/layout/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in GFA v1.0 format or in ODGI binary format pattern: "*.{gfa,og}" - output: - meta: type: map @@ -43,6 +41,7 @@ output: type: file description: File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified. pattern: "*.{tsv}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test b/modules/nf-core/odgi/layout/tests/main.nf.test new file mode 100644 index 00000000..67f915a3 --- /dev/null +++ b/modules/nf-core/odgi/layout/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process ODGI_LAYOUT" + script "../main.nf" + process "ODGI_LAYOUT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/layout" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, +// { assert snapshot(process.out).match() } // odgi layout is not deterministic + ) + } + + } + +} diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test.snap b/modules/nf-core/odgi/layout/tests/main.nf.test.snap new file mode 100644 index 00000000..df8dcf35 --- /dev/null +++ b/modules/nf-core/odgi/layout/tests/main.nf.test.snap @@ -0,0 +1,51 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.lay:md5,ce4ee2f434717077f5c765a5a82fd978" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,7bf353889ac6dfcce8b38618d760f144" + ] + ], + "2": [ + "versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b" + ], + "lay": [ + [ + { + "id": "test", + "single_end": false + }, + "test.lay:md5,ce4ee2f434717077f5c765a5a82fd978" + ] + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,7bf353889ac6dfcce8b38618d760f144" + ] + ], + "versions": [ + "versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b" + ] + } + ], + "timestamp": "2024-01-30T10:58:20.958731752" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/layout/tests/nextflow.config b/modules/nf-core/odgi/layout/tests/nextflow.config new file mode 100644 index 00000000..d1ba5054 --- /dev/null +++ b/modules/nf-core/odgi/layout/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: ODGI_LAYOUT { + ext.args = { "--out ${meta.id}.lay --tsv ${meta.id}.tsv" } + } + +} diff --git a/modules/nf-core/odgi/sort/environment.yml b/modules/nf-core/odgi/sort/environment.yml new file mode 100644 index 00000000..1c1abb89 --- /dev/null +++ b/modules/nf-core/odgi/sort/environment.yml @@ -0,0 +1,7 @@ +name: odgi_sort +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/sort/main.nf b/modules/nf-core/odgi/sort/main.nf index d57cc04a..06462495 100644 --- a/modules/nf-core/odgi/sort/main.nf +++ b/modules/nf-core/odgi/sort/main.nf @@ -2,10 +2,10 @@ process ODGI_SORT { tag "$meta.id" label 'process_high' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/sort/meta.yml b/modules/nf-core/odgi/sort/meta.yml index c29dd91c..792dc381 100644 --- a/modules/nf-core/odgi/sort/meta.yml +++ b/modules/nf-core/odgi/sort/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in GFA v1.0 format or in ODGI binary format pattern: "*.{gfa,og}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: 1D sorted pangenome graph in ODGI binary format pattern: "*.{og}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/sort/tests/main.nf.test b/modules/nf-core/odgi/sort/tests/main.nf.test new file mode 100644 index 00000000..8245c9e5 --- /dev/null +++ b/modules/nf-core/odgi/sort/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_SORT" + script "../main.nf" + process "ODGI_SORT" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/sort" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/sort/tests/main.nf.test.snap b/modules/nf-core/odgi/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..88bcc958 --- /dev/null +++ b/modules/nf-core/odgi/sort/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "1": [ + "versions.yml:md5,6defcba99b79fde2042de15eec929bf4" + ], + "sorted_graph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "versions": [ + "versions.yml:md5,6defcba99b79fde2042de15eec929bf4" + ] + } + ], + "timestamp": "2024-01-30T10:52:27.598708358" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/squeeze/environment.yml b/modules/nf-core/odgi/squeeze/environment.yml new file mode 100644 index 00000000..298458f0 --- /dev/null +++ b/modules/nf-core/odgi/squeeze/environment.yml @@ -0,0 +1,7 @@ +name: odgi_squeeze +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/squeeze/main.nf b/modules/nf-core/odgi/squeeze/main.nf index a2e187fe..6872fb65 100644 --- a/modules/nf-core/odgi/squeeze/main.nf +++ b/modules/nf-core/odgi/squeeze/main.nf @@ -2,10 +2,10 @@ process ODGI_SQUEEZE { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graphs) diff --git a/modules/nf-core/odgi/squeeze/meta.yml b/modules/nf-core/odgi/squeeze/meta.yml index 4b6181d3..5ffaa618 100644 --- a/modules/nf-core/odgi/squeeze/meta.yml +++ b/modules/nf-core/odgi/squeeze/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph files in ODGI format. pattern: "*.{og}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/squeeze/tests/main.nf.test b/modules/nf-core/odgi/squeeze/tests/main.nf.test new file mode 100644 index 00000000..05fb5a8d --- /dev/null +++ b/modules/nf-core/odgi/squeeze/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_SQUEEZE" + script "../main.nf" + process "ODGI_SQUEEZE" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/squeeze" + + test("homo_sapiens - pangenome - odgi - pangenome_og") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['odgi']['pangenome_og'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap b/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap new file mode 100644 index 00000000..2601eb12 --- /dev/null +++ b/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - odgi - pangenome_og": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "1": [ + "versions.yml:md5,ee7ed77636f98e98a3e40a915c22ed64" + ], + "graph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "versions": [ + "versions.yml:md5,ee7ed77636f98e98a3e40a915c22ed64" + ] + } + ], + "timestamp": "2024-01-30T10:48:02.189347916" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/stats/environment.yml b/modules/nf-core/odgi/stats/environment.yml new file mode 100644 index 00000000..e404f09f --- /dev/null +++ b/modules/nf-core/odgi/stats/environment.yml @@ -0,0 +1,7 @@ +name: odgi_stats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/stats/main.nf b/modules/nf-core/odgi/stats/main.nf index 99409f65..7848cfc3 100644 --- a/modules/nf-core/odgi/stats/main.nf +++ b/modules/nf-core/odgi/stats/main.nf @@ -2,10 +2,10 @@ process ODGI_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/stats/meta.yml b/modules/nf-core/odgi/stats/meta.yml index b80fb195..e8e26e02 100644 --- a/modules/nf-core/odgi/stats/meta.yml +++ b/modules/nf-core/odgi/stats/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in binary ODGI or in GFA v1.0 format pattern: "*.{og,gfa}" - output: - meta: type: map @@ -43,6 +41,7 @@ output: type: file description: Optional output file that contains graph statistics in YAML format. pattern: "*.{yaml}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/stats/tests/main.nf.test b/modules/nf-core/odgi/stats/tests/main.nf.test new file mode 100644 index 00000000..72e08774 --- /dev/null +++ b/modules/nf-core/odgi/stats/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_STATS" + script "../main.nf" + process "ODGI_STATS" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/stats" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/stats/tests/main.nf.test.snap b/modules/nf-core/odgi/stats/tests/main.nf.test.snap new file mode 100644 index 00000000..c7221489 --- /dev/null +++ b/modules/nf-core/odgi/stats/tests/main.nf.test.snap @@ -0,0 +1,39 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test..og.stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,0f4d685d1c0d3562081073bfbf85d95d" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test..og.stats.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0f4d685d1c0d3562081073bfbf85d95d" + ], + "yaml": [ + + ] + } + ], + "timestamp": "2024-01-30T10:45:11.453785835" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/unchop/environment.yml b/modules/nf-core/odgi/unchop/environment.yml new file mode 100644 index 00000000..1dadcdc9 --- /dev/null +++ b/modules/nf-core/odgi/unchop/environment.yml @@ -0,0 +1,7 @@ +name: odgi_unchop +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/unchop/main.nf b/modules/nf-core/odgi/unchop/main.nf index 50cbfde2..033011c4 100644 --- a/modules/nf-core/odgi/unchop/main.nf +++ b/modules/nf-core/odgi/unchop/main.nf @@ -2,10 +2,10 @@ process ODGI_UNCHOP { tag "$meta.id" label 'process_medium' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/unchop/meta.yml b/modules/nf-core/odgi/unchop/meta.yml index c704f863..5dc31f06 100644 --- a/modules/nf-core/odgi/unchop/meta.yml +++ b/modules/nf-core/odgi/unchop/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in GFA v1.0 format or in ODGI binary format pattern: "*.{gfa,og}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: Unchopped pangenome graph in ODGI binary format pattern: "*.{og}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/unchop/tests/main.nf.test b/modules/nf-core/odgi/unchop/tests/main.nf.test new file mode 100644 index 00000000..bc940498 --- /dev/null +++ b/modules/nf-core/odgi/unchop/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_UNCHOP" + script "../main.nf" + process "ODGI_UNCHOP" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/unchop" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/unchop/tests/main.nf.test.snap b/modules/nf-core/odgi/unchop/tests/main.nf.test.snap new file mode 100644 index 00000000..3f5082b2 --- /dev/null +++ b/modules/nf-core/odgi/unchop/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "1": [ + "versions.yml:md5,721a9406e96a94ccb0ec44dc4f76ed09" + ], + "unchopped_graph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.og:md5,91a02c7320969d66bc862cdea317e92e" + ] + ], + "versions": [ + "versions.yml:md5,721a9406e96a94ccb0ec44dc4f76ed09" + ] + } + ], + "timestamp": "2024-01-30T10:40:05.942092101" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/view/environment.yml b/modules/nf-core/odgi/view/environment.yml new file mode 100644 index 00000000..94bf48f5 --- /dev/null +++ b/modules/nf-core/odgi/view/environment.yml @@ -0,0 +1,7 @@ +name: odgi_view +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/view/main.nf b/modules/nf-core/odgi/view/main.nf index cecfe454..83672e4e 100644 --- a/modules/nf-core/odgi/view/main.nf +++ b/modules/nf-core/odgi/view/main.nf @@ -2,10 +2,10 @@ process ODGI_VIEW { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/view/meta.yml b/modules/nf-core/odgi/view/meta.yml index 68b1f17a..2b8b0d4d 100644 --- a/modules/nf-core/odgi/view/meta.yml +++ b/modules/nf-core/odgi/view/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in GFA v1.0 format or in ODGI binary format pattern: "*.{gfa,og}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: File containing a pangenome graph in GFA v1.0 format. pattern: "*.{gfa}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/view/tests/main.nf.test b/modules/nf-core/odgi/view/tests/main.nf.test new file mode 100644 index 00000000..534608aa --- /dev/null +++ b/modules/nf-core/odgi/view/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_VIEW" + script "../main.nf" + process "ODGI_VIEW" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/view" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/view/tests/main.nf.test.snap b/modules/nf-core/odgi/view/tests/main.nf.test.snap new file mode 100644 index 00000000..1d9fc967 --- /dev/null +++ b/modules/nf-core/odgi/view/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gfa:md5,f6c3da9f9317b4546cbb74ad35bf8726" + ] + ], + "1": [ + "versions.yml:md5,cda909193ec196138daed6da151a8e83" + ], + "gfa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gfa:md5,f6c3da9f9317b4546cbb74ad35bf8726" + ] + ], + "versions": [ + "versions.yml:md5,cda909193ec196138daed6da151a8e83" + ] + } + ], + "timestamp": "2024-01-30T10:35:28.605315319" + } +} \ No newline at end of file diff --git a/modules/nf-core/odgi/viz/environment.yml b/modules/nf-core/odgi/viz/environment.yml new file mode 100644 index 00000000..8931e0ec --- /dev/null +++ b/modules/nf-core/odgi/viz/environment.yml @@ -0,0 +1,7 @@ +name: odgi_viz +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/viz/main.nf b/modules/nf-core/odgi/viz/main.nf index feef5be2..562300eb 100644 --- a/modules/nf-core/odgi/viz/main.nf +++ b/modules/nf-core/odgi/viz/main.nf @@ -2,10 +2,10 @@ process ODGI_VIZ { tag "$meta.id" label 'process_single' - conda "bioconda::odgi=0.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.3--py310h6cc9453_0': - 'biocontainers/odgi:0.8.3--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': + 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/viz/meta.yml b/modules/nf-core/odgi/viz/meta.yml index 66fa8798..8f8a0370 100644 --- a/modules/nf-core/odgi/viz/meta.yml +++ b/modules/nf-core/odgi/viz/meta.yml @@ -12,8 +12,7 @@ tools: documentation: "https://odgi.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: Pangenome graph in binary ODGI or in GFA v1.0 format pattern: "*.{og,gfa}" - output: - meta: type: map @@ -39,6 +37,7 @@ output: type: file description: A 1D visualization of a pangenome graph. pattern: "*.{png}" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/odgi/viz/tests/main.nf.test b/modules/nf-core/odgi/viz/tests/main.nf.test new file mode 100644 index 00000000..e6a2d058 --- /dev/null +++ b/modules/nf-core/odgi/viz/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process ODGI_VIZ" + script "../main.nf" + process "ODGI_VIZ" + + tag "modules" + tag "modules_nfcore" + tag "odgi" + tag "odgi/viz" + + test("homo_sapiens - pangenome - pangenome_smoothxg_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_smoothxg_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/odgi/viz/tests/main.nf.test.snap b/modules/nf-core/odgi/viz/tests/main.nf.test.snap new file mode 100644 index 00000000..49e909ba --- /dev/null +++ b/modules/nf-core/odgi/viz/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.png:md5,45aad95d5e11a87c2f8c03ca703438bf" + ] + ], + "1": [ + "versions.yml:md5,95c0ee8015cf342c2724fb64d4cba67e" + ], + "png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.png:md5,45aad95d5e11a87c2f8c03ca703438bf" + ] + ], + "versions": [ + "versions.yml:md5,95c0ee8015cf342c2724fb64d4cba67e" + ] + } + ], + "timestamp": "2024-01-30T09:53:51.373368285" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 00000000..4807ba5f --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,8 @@ +name: samtools_faidx +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 59ed3088..d3461627 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 957b25e5..e189af28 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -55,3 +55,7 @@ authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/seqwish/induce/environment.yml b/modules/nf-core/seqwish/induce/environment.yml new file mode 100644 index 00000000..63711c0b --- /dev/null +++ b/modules/nf-core/seqwish/induce/environment.yml @@ -0,0 +1,7 @@ +name: seqwish_induce +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::seqwish=0.7.9 diff --git a/modules/nf-core/seqwish/induce/main.nf b/modules/nf-core/seqwish/induce/main.nf index 2a6a8ba5..f4517f95 100644 --- a/modules/nf-core/seqwish/induce/main.nf +++ b/modules/nf-core/seqwish/induce/main.nf @@ -2,7 +2,7 @@ process SEQWISH_INDUCE { tag "$meta.id" label 'process_medium' - conda "bioconda::seqwish=0.7.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqwish:0.7.9--h5b5514e_0' : 'biocontainers/seqwish:0.7.9--h5b5514e_0' }" diff --git a/modules/nf-core/seqwish/induce/meta.yml b/modules/nf-core/seqwish/induce/meta.yml index f6b92236..562f4014 100644 --- a/modules/nf-core/seqwish/induce/meta.yml +++ b/modules/nf-core/seqwish/induce/meta.yml @@ -28,7 +28,6 @@ input: type: file description: FASTA file used to generate alignments pattern: "*.{fa,fa.gz,fasta,fasta.gz}" - output: - meta: type: map @@ -45,3 +44,5 @@ output: pattern: "versions.yml" authors: - "@heuermh" +maintainers: + - "@heuermh" diff --git a/modules/nf-core/smoothxg/environment.yml b/modules/nf-core/smoothxg/environment.yml new file mode 100644 index 00000000..76ca4b86 --- /dev/null +++ b/modules/nf-core/smoothxg/environment.yml @@ -0,0 +1,7 @@ +name: smoothxg +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::smoothxg=0.7.2 diff --git a/modules/nf-core/smoothxg/main.nf b/modules/nf-core/smoothxg/main.nf index 0d10a4a4..191e14cd 100644 --- a/modules/nf-core/smoothxg/main.nf +++ b/modules/nf-core/smoothxg/main.nf @@ -2,10 +2,10 @@ process SMOOTHXG { tag "$meta.id" label 'process_high' - conda "bioconda::smoothxg=0.7.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/smoothxg:0.7.1--h40c17d1_0' : - 'biocontainers/smoothxg:0.7.1--h40c17d1_0' }" + 'https://depot.galaxyproject.org/singularity/smoothxg:0.7.2--h40c17d1_0' : + 'biocontainers/smoothxg:0.7.2--h40c17d1_0' }" input: tuple val(meta), path(gfa) diff --git a/modules/nf-core/smoothxg/meta.yml b/modules/nf-core/smoothxg/meta.yml index d6a744f0..2ba721f8 100644 --- a/modules/nf-core/smoothxg/meta.yml +++ b/modules/nf-core/smoothxg/meta.yml @@ -24,7 +24,6 @@ input: type: file description: Variation graph in GFA 1.0 format pattern: "*.{gfa}" - output: - meta: type: map @@ -45,3 +44,5 @@ output: pattern: "*.{maf}" authors: - "@heuermh, @subwaystation" +maintainers: + - "@heuermh, @subwaystation" diff --git a/modules/nf-core/smoothxg/tests/main.nf.test b/modules/nf-core/smoothxg/tests/main.nf.test new file mode 100644 index 00000000..ed19da0b --- /dev/null +++ b/modules/nf-core/smoothxg/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process SMOOTHXG" + script "../main.nf" + process "SMOOTHXG" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "smoothxg" + + test("sarscov2 - illumina - assembly_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, +// { assert snapshot(process.out).match() } // SMOOTHXG is never deterministic + ) + } + + } + + test("homo_sapiens - pangenome - pangenome_seqwish_gfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_seqwish_gfa'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, +// { assert snapshot(process.out).match() } // SMOOTHXG is never deterministic + ) + } + + } + +} diff --git a/modules/nf-core/smoothxg/tests/main.nf.test.snap b/modules/nf-core/smoothxg/tests/main.nf.test.snap new file mode 100644 index 00000000..34123620 --- /dev/null +++ b/modules/nf-core/smoothxg/tests/main.nf.test.snap @@ -0,0 +1,39 @@ +{ + "sarscov2 - illumina - assembly_gfa": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.smoothxg.gfa:md5,c85140490fb255f8361499c01d0dd15b" + ] + ], + "1": [ + "test.maf:md5,a6d82f572a5358926b87c69683d7825e" + ], + "2": [ + "versions.yml:md5,14c3d1a28b189a6db45facabbb5dc274" + ], + "gfa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.smoothxg.gfa:md5,c85140490fb255f8361499c01d0dd15b" + ] + ], + "maf": [ + "test.maf:md5,a6d82f572a5358926b87c69683d7825e" + ], + "versions": [ + "versions.yml:md5,14c3d1a28b189a6db45facabbb5dc274" + ] + } + ], + "timestamp": "2024-01-25T16:06:35.857843316" + } +} \ No newline at end of file diff --git a/modules/nf-core/smoothxg/tests/nextflow.config b/modules/nf-core/smoothxg/tests/nextflow.config new file mode 100644 index 00000000..2d2b27d9 --- /dev/null +++ b/modules/nf-core/smoothxg/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + + withName: SMOOTHXG { + ext.args = { + [ + "--write-msa-in-maf-format test.maf --n-haps 10" + ].join(" ").trim() + } + } + +} diff --git a/modules/nf-core/smoothxg/tests/tags.yml b/modules/nf-core/smoothxg/tests/tags.yml new file mode 100644 index 00000000..2089a657 --- /dev/null +++ b/modules/nf-core/smoothxg/tests/tags.yml @@ -0,0 +1,2 @@ +smoothxg: + - "modules/nf-core/smoothxg/**" diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml new file mode 100644 index 00000000..4fe40c56 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -0,0 +1,7 @@ +name: tabix_bgzip +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 8c47d9e2..7772e9ad 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -2,7 +2,7 @@ process TABIX_BGZIP { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'biocontainers/tabix:1.11--hdfd78af_0' }" diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index c3ea2107..621d49ea 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -45,3 +45,8 @@ authors: - "@drpatelh" - "@maxulysse" - "@nvnieuwk" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" + - "@nvnieuwk" diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml new file mode 100644 index 00000000..4e7e66c3 --- /dev/null +++ b/modules/nf-core/wfmash/environment.yml @@ -0,0 +1,7 @@ +name: wfmash +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::wfmash=0.12.5 diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf index 0f9c5818..3e1592f4 100644 --- a/modules/nf-core/wfmash/main.nf +++ b/modules/nf-core/wfmash/main.nf @@ -2,10 +2,10 @@ process WFMASH { tag "$meta.id" label 'process_medium' - conda "bioconda::wfmash=0.10.5" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wfmash:0.10.5--h94f6cfe_0': - 'biocontainers/wfmash:0.10.5--h94f6cfe_0' }" + 'https://depot.galaxyproject.org/singularity/wfmash:0.12.5--h11f254b_0': + 'biocontainers/wfmash:0.12.5--h11f254b_0' }" input: tuple val(meta), path(fasta_gz), path(paf), path(gzi), path(fai) diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index 80e630cc..dc5cd5a8 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -13,8 +13,7 @@ tools: documentation: https://github.com/waveygang/wfmash tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 - licence: "['MIT']" - + licence: ["MIT"] input: - meta: type: map @@ -44,7 +43,6 @@ input: type: file description: Optional inpute file in FASTA format specifying the query sequences as a list. pattern: "*.{fa,fna,fasta}" - output: - meta: type: map @@ -59,6 +57,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@subwaystation" +maintainers: + - "@subwaystation" diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test new file mode 100644 index 00000000..41d8c23c --- /dev/null +++ b/modules/nf-core/wfmash/tests/main.nf.test @@ -0,0 +1,39 @@ +nextflow_process { + + name "Test Process WFMASH" + script "../main.nf" + process "WFMASH" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "wfmash" + + test("homo_sapiens - pangenome - pangenome_fa_bgzip") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip'], checkIfExists: true), + [], // empty paf input + file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_gzi'], checkIfExists: true), // gzi + file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_fai'], checkIfExists: true) // fai + ] + input[1] = true // empty paf input + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, +// { assert snapshot(process.out).exists() } // if run on more than 1 thread the lines in the resulting PAF will appear in a different order + ) + } + + } + +} diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap new file mode 100644 index 00000000..97a51e44 --- /dev/null +++ b/modules/nf-core/wfmash/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "homo_sapiens - pangenome - pangenome_fa_bgzip": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" + ] + ], + "1": [ + "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" + ], + "paf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" + ] + ], + "versions": [ + "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" + ] + } + ], + "timestamp": "2024-01-25T15:12:21.284828212" + } +} \ No newline at end of file diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config new file mode 100644 index 00000000..b7e9c989 --- /dev/null +++ b/modules/nf-core/wfmash/tests/nextflow.config @@ -0,0 +1,12 @@ +process { + + withName: WFMASH { + ext.args = { + [ + "-s 500", // necessary because of https://github.com/waveygang/wfmash/issues/218 + "-X" + ].join(" ").trim() + } + } + +} diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml new file mode 100644 index 00000000..7001b087 --- /dev/null +++ b/modules/nf-core/wfmash/tests/tags.yml @@ -0,0 +1,2 @@ +wfmash: + - "modules/nf-core/wfmash/**" From ef4996583e8179c8abe357296206a830f8339191 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 1 Feb 2024 15:39:56 +0100 Subject: [PATCH 2/3] revert wfmash to 0.10.5 --- modules.json | 2 +- modules/nf-core/wfmash/main.nf | 6 +++--- modules/nf-core/wfmash/meta.yml | 4 +--- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/modules.json b/modules.json index 7b0774ba..fb1833c0 100644 --- a/modules.json +++ b/modules.json @@ -87,7 +87,7 @@ }, "wfmash": { "branch": "master", - "git_sha": "8cbeaa5063f08952682517597d4e8d6e35bbcd1a", + "git_sha": "96fadda088c6e79777ba8eef939e36bb03a69c65", "installed_by": ["modules"] } } diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf index 3e1592f4..0f9c5818 100644 --- a/modules/nf-core/wfmash/main.nf +++ b/modules/nf-core/wfmash/main.nf @@ -2,10 +2,10 @@ process WFMASH { tag "$meta.id" label 'process_medium' - conda "${moduleDir}/environment.yml" + conda "bioconda::wfmash=0.10.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/wfmash:0.12.5--h11f254b_0': - 'biocontainers/wfmash:0.12.5--h11f254b_0' }" + 'https://depot.galaxyproject.org/singularity/wfmash:0.10.5--h94f6cfe_0': + 'biocontainers/wfmash:0.10.5--h94f6cfe_0' }" input: tuple val(meta), path(fasta_gz), path(paf), path(gzi), path(fai) diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index dc5cd5a8..1063f8b5 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/waveygang/wfmash tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 - licence: ["MIT"] + licence: "['MIT']" input: - meta: type: map @@ -59,5 +59,3 @@ output: pattern: "versions.yml" authors: - "@subwaystation" -maintainers: - - "@subwaystation" From a78db057ee409865b358eacbecff5da398134a39 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 1 Feb 2024 15:57:53 +0100 Subject: [PATCH 3/3] now --- modules/nf-core/wfmash/environment.yml | 7 ---- modules/nf-core/wfmash/meta.yml | 3 ++ modules/nf-core/wfmash/tests/main.nf.test | 39 ------------------- .../nf-core/wfmash/tests/main.nf.test.snap | 33 ---------------- modules/nf-core/wfmash/tests/nextflow.config | 12 ------ modules/nf-core/wfmash/tests/tags.yml | 2 - 6 files changed, 3 insertions(+), 93 deletions(-) delete mode 100644 modules/nf-core/wfmash/environment.yml delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test delete mode 100644 modules/nf-core/wfmash/tests/main.nf.test.snap delete mode 100644 modules/nf-core/wfmash/tests/nextflow.config delete mode 100644 modules/nf-core/wfmash/tests/tags.yml diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml deleted file mode 100644 index 4e7e66c3..00000000 --- a/modules/nf-core/wfmash/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: wfmash -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::wfmash=0.12.5 diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index 1063f8b5..80e630cc 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -14,6 +14,7 @@ tools: tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 licence: "['MIT']" + input: - meta: type: map @@ -43,6 +44,7 @@ input: type: file description: Optional inpute file in FASTA format specifying the query sequences as a list. pattern: "*.{fa,fna,fasta}" + output: - meta: type: map @@ -57,5 +59,6 @@ output: type: file description: File containing software versions pattern: "versions.yml" + authors: - "@subwaystation" diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test deleted file mode 100644 index 41d8c23c..00000000 --- a/modules/nf-core/wfmash/tests/main.nf.test +++ /dev/null @@ -1,39 +0,0 @@ -nextflow_process { - - name "Test Process WFMASH" - script "../main.nf" - process "WFMASH" - config "./nextflow.config" - - tag "modules" - tag "modules_nfcore" - tag "wfmash" - - test("homo_sapiens - pangenome - pangenome_fa_bgzip") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip'], checkIfExists: true), - [], // empty paf input - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_gzi'], checkIfExists: true), // gzi - file(params.test_data['homo_sapiens']['pangenome']['pangenome_fa_bgzip_fai'], checkIfExists: true) // fai - ] - input[1] = true // empty paf input - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, -// { assert snapshot(process.out).exists() } // if run on more than 1 thread the lines in the resulting PAF will appear in a different order - ) - } - - } - -} diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap deleted file mode 100644 index 97a51e44..00000000 --- a/modules/nf-core/wfmash/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "homo_sapiens - pangenome - pangenome_fa_bgzip": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" - ] - ], - "1": [ - "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" - ], - "paf": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paf:md5,aa6629548e32b2d036c0767c9086a6dd" - ] - ], - "versions": [ - "versions.yml:md5,0da45b7a6424a967e2f39225fb020140" - ] - } - ], - "timestamp": "2024-01-25T15:12:21.284828212" - } -} \ No newline at end of file diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config deleted file mode 100644 index b7e9c989..00000000 --- a/modules/nf-core/wfmash/tests/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -process { - - withName: WFMASH { - ext.args = { - [ - "-s 500", // necessary because of https://github.com/waveygang/wfmash/issues/218 - "-X" - ].join(" ").trim() - } - } - -} diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml deleted file mode 100644 index 7001b087..00000000 --- a/modules/nf-core/wfmash/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -wfmash: - - "modules/nf-core/wfmash/**"