diff --git a/modules.json b/modules.json index fbaa60c..8d81103 100644 --- a/modules.json +++ b/modules.json @@ -7,92 +7,92 @@ "nf-core": { "bwa/aln": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["fastq_align_bwaaln", "modules"] }, "bwa/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bwa/sampe": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e", "installed_by": ["fastq_align_bwaaln"] }, "bwa/samse": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e", "installed_by": ["fastq_align_bwaaln"] }, "cat/fastq": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "deeptools/bamcoverage": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", + "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006", "installed_by": ["bam_markduplicates_picard", "modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["bam_markduplicates_picard", "fastq_align_bwaaln"] }, "samtools/stats": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006", "installed_by": ["bam_stats_samtools"] }, "trimmomatic": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", "installed_by": ["modules"] } } @@ -101,17 +101,17 @@ "nf-core": { "bam_markduplicates_picard": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647", "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647", "installed_by": ["bam_markduplicates_picard"] }, "fastq_align_bwaaln": { "branch": "master", - "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", + "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bwa/aln/environment.yml b/modules/nf-core/bwa/aln/environment.yml new file mode 100644 index 0000000..c63d9e1 --- /dev/null +++ b/modules/nf-core/bwa/aln/environment.yml @@ -0,0 +1,7 @@ +name: bwa_aln +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf index 012e029..a537797 100644 --- a/modules/nf-core/bwa/aln/main.nf +++ b/modules/nf-core/bwa/aln/main.nf @@ -2,7 +2,7 @@ process BWA_ALN { tag "$meta.id" label 'process_medium' - conda "bioconda::bwa=0.7.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8' : 'biocontainers/bwa:0.7.17--h5bf99c6_8' }" diff --git a/modules/nf-core/bwa/aln/meta.yml b/modules/nf-core/bwa/aln/meta.yml index f4cc8f3..08eb538 100644 --- a/modules/nf-core/bwa/aln/meta.yml +++ b/modules/nf-core/bwa/aln/meta.yml @@ -18,7 +18,6 @@ tools: documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] - input: - meta: type: map @@ -39,7 +38,6 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - output: - meta: type: map @@ -54,6 +52,7 @@ output: type: file description: Single or paired SA coordinate files pattern: "*.sai" - authors: - "@jfy133" +maintainers: + - "@jfy133" diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test b/modules/nf-core/bwa/aln/tests/main.nf.test new file mode 100644 index 0000000..5d3d728 --- /dev/null +++ b/modules/nf-core/bwa/aln/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process BWA_ALN" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/aln" + script "../main.nf" + process "BWA_ALN" + + test("Single-End") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Paired-End") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test.snap b/modules/nf-core/bwa/aln/tests/main.nf.test.snap new file mode 100644 index 0000000..d9bf16a --- /dev/null +++ b/modules/nf-core/bwa/aln/tests/main.nf.test.snap @@ -0,0 +1,70 @@ +{ + "Single-End": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sai:md5,aaaf39b6814c96ca1a5eacc662adf926" + ] + ], + "1": [ + "versions.yml:md5,8b90409bc607b4179956d9c4217eb524" + ], + "sai": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sai:md5,aaaf39b6814c96ca1a5eacc662adf926" + ] + ], + "versions": [ + "versions.yml:md5,8b90409bc607b4179956d9c4217eb524" + ] + } + ], + "timestamp": "2023-10-18T11:14:33.203898589" + }, + "Paired-End": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.1.sai:md5,aaaf39b6814c96ca1a5eacc662adf926", + "test.2.sai:md5,b4f185d9b4cb256dd5c377070a536124" + ] + ] + ], + "1": [ + "versions.yml:md5,8b90409bc607b4179956d9c4217eb524" + ], + "sai": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.1.sai:md5,aaaf39b6814c96ca1a5eacc662adf926", + "test.2.sai:md5,b4f185d9b4cb256dd5c377070a536124" + ] + ] + ], + "versions": [ + "versions.yml:md5,8b90409bc607b4179956d9c4217eb524" + ] + } + ], + "timestamp": "2023-10-18T11:14:39.443861611" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/aln/tests/tags.yml b/modules/nf-core/bwa/aln/tests/tags.yml new file mode 100644 index 0000000..1258ff4 --- /dev/null +++ b/modules/nf-core/bwa/aln/tests/tags.yml @@ -0,0 +1,3 @@ +bwa/aln: + - modules/nf-core/bwa/aln/** + - modules/nf-core/bwa/index/** diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml new file mode 100644 index 0000000..5d3cb32 --- /dev/null +++ b/modules/nf-core/bwa/index/environment.yml @@ -0,0 +1,7 @@ +name: bwa_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 8d2e56d..24b5a2e 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ process BWA_INDEX { tag "$fasta" label 'process_single' - conda "bioconda::bwa=0.7.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : 'biocontainers/bwa:0.7.17--hed695b0_7' }" @@ -18,13 +18,14 @@ process BWA_INDEX { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${fasta.baseName}" + def args = task.ext.args ?: '' """ mkdir bwa bwa \\ index \\ $args \\ - -p bwa/${fasta.baseName} \\ + -p bwa/${prefix} \\ $fasta cat <<-END_VERSIONS > versions.yml @@ -34,14 +35,15 @@ process BWA_INDEX { """ stub: + def prefix = task.ext.prefix ?: "${fasta.baseName}" """ mkdir bwa - touch bwa/genome.amb - touch bwa/genome.ann - touch bwa/genome.bwt - touch bwa/genome.pac - touch bwa/genome.sa + touch bwa/${prefix}.amb + touch bwa/${prefix}.ann + touch bwa/${prefix}.bwt + touch bwa/${prefix}.pac + touch bwa/${prefix}.sa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 2c6cfcd..730628d 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -40,3 +40,6 @@ output: authors: - "@drpatelh" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test new file mode 100644 index 0000000..5fc8d49 --- /dev/null +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_process { + + name "Test Process BWA_INDEX" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/index" + script "../main.nf" + process "BWA_INDEX" + + test("BWA index") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap new file mode 100644 index 0000000..e51ad5b --- /dev/null +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -0,0 +1,43 @@ +{ + "BWA index": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "1": [ + "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "versions": [ + "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + ] + } + ], + "timestamp": "2023-10-17T17:20:20.180927714" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/index/tests/tags.yml b/modules/nf-core/bwa/index/tests/tags.yml new file mode 100644 index 0000000..28bb483 --- /dev/null +++ b/modules/nf-core/bwa/index/tests/tags.yml @@ -0,0 +1,2 @@ +bwa/index: + - modules/nf-core/bwa/index/** diff --git a/modules/nf-core/bwa/sampe/environment.yml b/modules/nf-core/bwa/sampe/environment.yml new file mode 100644 index 0000000..63bbd0b --- /dev/null +++ b/modules/nf-core/bwa/sampe/environment.yml @@ -0,0 +1,9 @@ +name: bwa_sampe +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/bwa/sampe/main.nf b/modules/nf-core/bwa/sampe/main.nf index 45bfffb..8b0f51d 100644 --- a/modules/nf-core/bwa/sampe/main.nf +++ b/modules/nf-core/bwa/sampe/main.nf @@ -2,10 +2,10 @@ process BWA_SAMPE { tag "$meta.id" label 'process_medium' - conda "bioconda::bwa=0.7.17 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' : - 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' : + 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/sampe/meta.yml b/modules/nf-core/bwa/sampe/meta.yml index 0cefb96..48a0737 100644 --- a/modules/nf-core/bwa/sampe/meta.yml +++ b/modules/nf-core/bwa/sampe/meta.yml @@ -19,7 +19,6 @@ tools: documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] - input: - meta: type: map @@ -43,7 +42,6 @@ input: type: directory description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX pattern: "bwa/" - output: - meta: type: map @@ -58,6 +56,7 @@ output: type: file description: BAM file pattern: "*.bam" - authors: - "@jfy133" +maintainers: + - "@jfy133" diff --git a/modules/nf-core/bwa/sampe/tests/main.nf.test b/modules/nf-core/bwa/sampe/tests/main.nf.test new file mode 100644 index 0000000..8f84d8a --- /dev/null +++ b/modules/nf-core/bwa/sampe/tests/main.nf.test @@ -0,0 +1,73 @@ +nextflow_process { + + name "Test Process BWA_SAMPE" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/sampe" + tag "bwa/aln" + tag "bwa/index" + script "../main.nf" + process "BWA_SAMPE" + + test("SamPE") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + run("BWA_ALN") { + script "../../aln/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BWA_INDEX.out.index + """ + } + } + } + + when { + process { + """ + input[0] = Channel + .fromList( + [ + [ id:'test', single_end:false ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + ) + .collect() + .join(BWA_ALN.out.sai) + input[1] = BWA_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwa/sampe/tests/main.nf.test.snap b/modules/nf-core/bwa/sampe/tests/main.nf.test.snap new file mode 100644 index 0000000..43309fe --- /dev/null +++ b/modules/nf-core/bwa/sampe/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "SamPE": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "bam": [ + + ], + "versions": [ + + ] + } + ], + "timestamp": "2023-10-18T11:35:44.254349331" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/sampe/tests/tags.yml b/modules/nf-core/bwa/sampe/tests/tags.yml new file mode 100644 index 0000000..dc65276 --- /dev/null +++ b/modules/nf-core/bwa/sampe/tests/tags.yml @@ -0,0 +1,4 @@ +bwa/sampe: + - modules/nf-core/bwa/aln/** + - modules/nf-core/bwa/index/** + - modules/nf-core/bwa/sampe/** diff --git a/modules/nf-core/bwa/samse/environment.yml b/modules/nf-core/bwa/samse/environment.yml new file mode 100644 index 0000000..d427a73 --- /dev/null +++ b/modules/nf-core/bwa/samse/environment.yml @@ -0,0 +1,9 @@ +name: bwa_samse +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bwa=0.7.17 + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/bwa/samse/main.nf b/modules/nf-core/bwa/samse/main.nf index 38752ed..8de45bf 100644 --- a/modules/nf-core/bwa/samse/main.nf +++ b/modules/nf-core/bwa/samse/main.nf @@ -2,10 +2,10 @@ process BWA_SAMSE { tag "$meta.id" label 'process_medium' - conda "bioconda::bwa=0.7.17 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' : - 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:219b6c272b25e7e642ae3ff0bf0c5c81a5135ab4-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' : + 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' }" input: tuple val(meta), path(reads), path(sai) diff --git a/modules/nf-core/bwa/samse/meta.yml b/modules/nf-core/bwa/samse/meta.yml index 1deab21..a366a24 100644 --- a/modules/nf-core/bwa/samse/meta.yml +++ b/modules/nf-core/bwa/samse/meta.yml @@ -10,7 +10,6 @@ keywords: - map - sam - bam - tools: - bwa: description: | @@ -20,7 +19,6 @@ tools: documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] - input: - meta: type: map @@ -44,7 +42,6 @@ input: type: directory description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX pattern: "bwa/" - output: - meta: type: map @@ -59,6 +56,7 @@ output: type: file description: BAM file pattern: "*.bam" - authors: - "@jfy133" +maintainers: + - "@jfy133" diff --git a/modules/nf-core/bwa/samse/tests/main.nf.test b/modules/nf-core/bwa/samse/tests/main.nf.test new file mode 100644 index 0000000..dcf8614 --- /dev/null +++ b/modules/nf-core/bwa/samse/tests/main.nf.test @@ -0,0 +1,67 @@ +nextflow_process { + + name "Test Process BWA_SAMSE" + tag "modules_nfcore" + tag "modules" + tag "bwa" + tag "bwa/samse" + tag "bwa/aln" + tag "bwa/index" + script "../main.nf" + process "BWA_SAMSE" + + test("SamSE") { + + setup { + run("BWA_INDEX") { + script "../../index/main.nf" + process { + """ + input[0] = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + run("BWA_ALN") { + script "../../aln/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BWA_INDEX.out.index + """ + } + } + } + + when { + process { + """ + input[0] = Channel + .fromList( + [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ) + .collect() + .join(BWA_ALN.out.sai) + input[1] = BWA_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwa/samse/tests/main.nf.test.snap b/modules/nf-core/bwa/samse/tests/main.nf.test.snap new file mode 100644 index 0000000..8526b40 --- /dev/null +++ b/modules/nf-core/bwa/samse/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "SamSE": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "bam": [ + + ], + "versions": [ + + ] + } + ], + "timestamp": "2023-10-18T11:34:27.527894872" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwa/samse/tests/tags.yml b/modules/nf-core/bwa/samse/tests/tags.yml new file mode 100644 index 0000000..9abcbd4 --- /dev/null +++ b/modules/nf-core/bwa/samse/tests/tags.yml @@ -0,0 +1,4 @@ +bwa/samse: + - modules/nf-core/bwa/aln/** + - modules/nf-core/bwa/index/** + - modules/nf-core/bwa/samse/** diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 0000000..bff93ad --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,7 @@ +name: cat_fastq +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6f..3d96378 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index 8a39e30..db4ac3c 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -34,7 +34,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@joseespinosa" - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 0000000..dab2e14 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,138 @@ +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // 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 snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // 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_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', 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 snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 0000000..43dfe28 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,169 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:30:39.816981" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:32:35.229332" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:34:00.058829" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:33:33.031555" + }, + "test_cat_fastq_paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:32:02.270935" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 0000000..6ac4361 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/functions.nf b/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/functions.nf deleted file mode 100644 index 85628ee..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/functions.nf +++ /dev/null @@ -1,78 +0,0 @@ -// -// Utility functions used in nf-core DSL2 module files -// - -// -// Extract name of software tool from process name using $task.process -// -def getSoftwareName(task_process) { - return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() -} - -// -// Extract name of module from process name using $task.process -// -def getProcessName(task_process) { - return task_process.tokenize(':')[-1] -} - -// -// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules -// -def initOptions(Map args) { - def Map options = [:] - options.args = args.args ?: '' - options.args2 = args.args2 ?: '' - options.args3 = args.args3 ?: '' - options.publish_by_meta = args.publish_by_meta ?: [] - options.publish_dir = args.publish_dir ?: '' - options.publish_files = args.publish_files - options.suffix = args.suffix ?: '' - return options -} - -// -// Tidy up and join elements of a list to return a path string -// -def getPathFromList(path_list) { - def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries - paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes - return paths.join('/') -} - -// -// Function to save/publish module results -// -def saveFiles(Map args) { - def ioptions = initOptions(args.options) - def path_list = [ ioptions.publish_dir ?: args.publish_dir ] - - // Do not publish versions.yml unless running from pytest workflow - if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { - return null - } - if (ioptions.publish_by_meta) { - def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta - for (key in key_list) { - if (args.meta && key instanceof String) { - def path = key - if (args.meta.containsKey(key)) { - path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key] - } - path = path instanceof String ? path : '' - path_list.add(path) - } - } - } - if (ioptions.publish_files instanceof Map) { - for (ext in ioptions.publish_files) { - if (args.filename.endsWith(ext.key)) { - def ext_list = path_list.collect() - ext_list.add(ext.value) - return "${getPathFromList(ext_list)}/$args.filename" - } - } - } else if (ioptions.publish_files == null) { - return "${getPathFromList(path_list)}/$args.filename" - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/main.nf deleted file mode 100644 index faf2073..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,106 +0,0 @@ -// Import generic module functions -include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' - -params.options = [:] -options = initOptions(params.options) - -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_low' - publishDir "${params.outdir}", - mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) } - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? "bioconda::multiqc=1.11" : null) - if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0" - } else { - container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0" - } - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - script: - """ - #!/usr/bin/env python - - import yaml - import platform - from textwrap import dedent - - def _make_versions_html(versions): - html = [ - dedent( - '''\\ - - - - - - - - - - ''' - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f'''\\ - - - - - - ''' - ) - ) - html.append("") - html.append("
Process Name Software Version
{process if (i == 0) else ''}{tool}{version}
") - return "\\n".join(html) - - module_versions = {} - module_versions["${getProcessName(task.process)}"] = { - 'python': platform.python_version(), - 'yaml': yaml.__version__ - } - - with open("$versions") as f: - workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions - - workflow_versions["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version" - } - - versions_mqc = { - 'id': 'software_versions', - 'section_name': '${workflow.manifest.name} Software Versions', - 'section_href': 'https://github.com/${workflow.manifest.name}', - 'plot_type': 'html', - 'description': 'are collected at run time from the software output.', - 'data': _make_versions_html(workflow_versions) - } - - with open("software_versions.yml", 'w') as f: - yaml.dump(workflow_versions, f, default_flow_style=False) - with open("software_versions_mqc.yml", 'w') as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open('versions.yml', 'w') as f: - yaml.dump(module_versions, f, default_flow_style=False) - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/meta.yml deleted file mode 100644 index 8d4a6ed..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,33 +0,0 @@ -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" - -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@drpatelh" diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 0000000..9b3272b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc8727..f218761 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657d..5f15a5f 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index e55b8d4..da03340 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,11 +4,10 @@ """Provide functions to merge multiple versions.yml files.""" +import yaml import platform from textwrap import dedent -import yaml - def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 0000000..b1e1630 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 0000000..5f59a93 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 0000000..405aa24 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/deeptools/bamcoverage/environment.yml b/modules/nf-core/deeptools/bamcoverage/environment.yml new file mode 100644 index 0000000..345ac70 --- /dev/null +++ b/modules/nf-core/deeptools/bamcoverage/environment.yml @@ -0,0 +1,8 @@ +name: deeptools_bamcoverage +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::deeptools=3.5.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/deeptools/bamcoverage/main.nf b/modules/nf-core/deeptools/bamcoverage/main.nf index 680fc5b..8aff5d6 100644 --- a/modules/nf-core/deeptools/bamcoverage/main.nf +++ b/modules/nf-core/deeptools/bamcoverage/main.nf @@ -2,7 +2,7 @@ process DEEPTOOLS_BAMCOVERAGE { tag "$meta.id" label 'process_low' - conda "bioconda::deeptools=3.5.1 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:62d1ebe2d3a2a9d1a7ad31e0b902983fa7c25fa7-0': 'biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:62d1ebe2d3a2a9d1a7ad31e0b902983fa7c25fa7-0' }" diff --git a/modules/nf-core/deeptools/bamcoverage/meta.yml b/modules/nf-core/deeptools/bamcoverage/meta.yml index 769592c..e8043e9 100644 --- a/modules/nf-core/deeptools/bamcoverage/meta.yml +++ b/modules/nf-core/deeptools/bamcoverage/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/deeptools/deepTools/ doi: "10.1093/nar/gkw257" licence: ["GPL v3"] - input: - meta: type: map @@ -35,7 +34,6 @@ input: type: file description: Index of the reference file (optional, but recommended) pattern: "*.{fai}" - output: - meta: type: map @@ -54,7 +52,9 @@ output: type: file description: Bedgraph file pattern: "*.bedgraph" - authors: - "@FriederikeHanssen" - "@SusiJo" +maintainers: + - "@FriederikeHanssen" + - "@SusiJo" diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 0000000..1787b38 --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 67209f7..9e19a74 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.12.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5..ee5507e 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index badb671..70edae4 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -1,25 +1,22 @@ nextflow_process { name "Test Process FASTQC" - script "modules/nf-core/fastqc/main.nf" + script "../main.nf" process "FASTQC" - tag "fastqc" + + tag "modules" tag "modules_nfcore" + tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) """ } } @@ -27,14 +24,189 @@ nextflow_process { 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.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + + { 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("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_single") } + ) + } + } + + 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("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } + + 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("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + ) + } + } + + 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("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + ) + } + } + + 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("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + ) + } + } + + 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("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + ) + } + } + + 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("fastqc_stub") } + ) + } + } + } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32c..86f7c31 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,88 @@ { - "versions": { + "fastqc_versions_interleaved": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" + }, + "fastqc_versions_custom_prefix": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 0000000..7834294 --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 0000000..25910b3 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +name: gunzip +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 73bf08c..468a6f2 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -2,7 +2,7 @@ process GUNZIP { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4cdcdf4..231034f 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -33,3 +33,7 @@ authors: - "@joseespinosa" - "@drpatelh" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 0000000..6406008 --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + 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).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..720fd9f --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "timestamp": "2023-10-17T15:35:37.690477896" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 0000000..7625b75 --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0..1b9f7c4 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml @@ -41,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee..45a9bc3 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +12,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +29,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +51,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 0000000..f1c4242 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,84 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("sarscov2 single-end [fastqc]") { + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("multiqc_versions_single") } + ) + } + + } + + test("sarscov2 single-end [fastqc] [config]") { + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("multiqc_versions_config") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match("multiqc_stub") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 0000000..549ba79 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "multiqc_versions_single": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:43:40.529579" + }, + "multiqc_stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:45:09.605359" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:44:53.535994" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 0000000..bea6c0d --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml new file mode 100644 index 0000000..58b795f --- /dev/null +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -0,0 +1,7 @@ +name: picard_markduplicates +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index facd7ef..80930cc 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=3.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : + 'biocontainers/picard:3.1.1--hdfd78af_0' }" input: tuple val(meta), path(bam) @@ -30,6 +30,9 @@ process PICARD_MARKDUPLICATES { } else { avail_mem = (task.memory.mega*0.8).intValue() } + + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ picard \\ -Xmx${avail_mem}M \\ @@ -48,6 +51,7 @@ process PICARD_MARKDUPLICATES { stub: def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.bam touch ${prefix}.bam.bai diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index f7693d2..1ab90c0 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -69,3 +69,7 @@ authors: - "@drpatelh" - "@projectoriented" - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test new file mode 100644 index 0000000..c5a29b4 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -0,0 +1,104 @@ +nextflow_process { + + name "Test Process PICARD_MARKDUPLICATES" + script "../main.nf" + process "PICARD_MARKDUPLICATES" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/markduplicates" + + test("sarscov2 [unsorted 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.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("unsorted_bam_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("unsorted_bam_metrics") }, + { assert snapshot(process.out.versions).match("unsorted_bam_versions") } + ) + } + } + + test("sarscov2 [sorted 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) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("sorted_bam_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("sorted_bam_metrics") }, + { assert snapshot(process.out.versions).match("sorted_bam_versions") } + ) + } + } + + test("homo_sapiens [cram]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("cram_metrics") }, + { assert snapshot(process.out.versions).match("cram_versions") } + ) + } + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap new file mode 100644 index 0000000..31c9130 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "sorted_bam_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "timestamp": "2024-01-19T10:26:45.092349" + }, + "unsorted_bam_name": { + "content": [ + "test.marked.bam" + ], + "timestamp": "2024-01-19T10:26:28.100755" + }, + "cram_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "timestamp": "2024-01-19T10:27:03.253071" + }, + "sorted_bam_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "timestamp": "2024-01-19T10:26:45.086503" + }, + "cram_name": { + "content": [ + "test.marked.bam" + ], + "timestamp": "2024-01-19T10:27:03.241617" + }, + "cram_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "timestamp": "2024-01-19T10:27:03.26989" + }, + "unsorted_bam_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "timestamp": "2024-01-19T10:26:28.159071" + }, + "unsorted_bam_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "timestamp": "2024-01-19T10:26:28.143979" + }, + "sorted_bam_name": { + "content": [ + "test.marked.bam" + ], + "timestamp": "2024-01-19T10:26:45.080116" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config new file mode 100644 index 0000000..02818dd --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: PICARD_MARKDUPLICATES { + ext.prefix = { "${meta.id}.marked" } + ext.args = '--ASSUME_SORT_ORDER queryname' + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml new file mode 100644 index 0000000..4f213d6 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/tags.yml @@ -0,0 +1,2 @@ +picard/markduplicates: + - modules/nf-core/picard/markduplicates/** diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 0000000..4807ba5 --- /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 59ed308..d346162 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 957b25e..e189af2 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -55,3 +55,7 @@ authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml new file mode 100644 index 0000000..dd0b5c1 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -0,0 +1,8 @@ +name: samtools_flagstat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b75707e..f1893d7 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" 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(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 954225d..9799135 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -47,3 +47,5 @@ output: pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test new file mode 100644 index 0000000..c8dd8dc --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FLAGSTAT" + script "../main.nf" + process "SAMTOOLS_FLAGSTAT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/flagstat" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.flagstat).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap new file mode 100644 index 0000000..880019f --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "timestamp": "2023-11-14T15:49:22.577133" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml new file mode 100644 index 0000000..2d2b725 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml new file mode 100644 index 0000000..de3ed47 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -0,0 +1,8 @@ +name: samtools_idxstats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 83c7c34..00d916b 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" 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(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index dda87e1..344e92a 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -48,3 +48,5 @@ output: pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test new file mode 100644 index 0000000..f6c9215 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_IDXSTATS" + script "../main.nf" + process "SAMTOOLS_IDXSTATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/idxstats" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.idxstats).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap new file mode 100644 index 0000000..4c6c12b --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2023-11-14T15:52:19.875194" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml new file mode 100644 index 0000000..d3057c6 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 0000000..81f0939 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,8 @@ +name: samtools_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4..8ad18fd 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - 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(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 8bd2fa6..01a4ee0 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -51,3 +51,7 @@ authors: - "@drpatelh" - "@ewels" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 0000000..0ed260e --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 0000000..c76a916 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("sarscov2 [BAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CRAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CSI]") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 0000000..b3baee7 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "crai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "timestamp": "2023-11-15T15:17:37.30801" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "timestamp": "2023-11-15T15:17:30.869234" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 0000000..e0f58a7 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 0000000..b45ba90 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,8 @@ +name: samtools_stats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4a2607d..7539140 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_STATS { tag "$meta.id" 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(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 90e6345..735ff81 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -57,3 +57,7 @@ authors: - "@drpatelh" - "@FriederikeHanssen" - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test new file mode 100644 index 0000000..20c3efe --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -0,0 +1,78 @@ +nextflow_process { + + name "Test Process SAMTOOLS_STATS" + script "../main.nf" + process "SAMTOOLS_STATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/stats" + + test("SAMTOOLS STATS Should run without failures") { + + when { + params { + + outdir = "$outputDir" + } + process { + """ + // define inputs of the process here. + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + + ] + input[1] = [[],[]] + """ + + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + + } + + test("SAMTOOLS CRAM Should run without failures") { + + when { + params { + + outdir = "$outputDir" + } + process { + """ + // define inputs of the process here + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) + + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + + + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + + } + + +} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap new file mode 100644 index 0000000..025c83a --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "SAMTOOLS STATS Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + ] + ], + "1": [ + "versions.yml:md5,650a365c6635001436008350ae83337c" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + ] + ], + "versions": [ + "versions.yml:md5,650a365c6635001436008350ae83337c" + ] + } + ], + "timestamp": "2023-12-04T11:07:28.26821485" + }, + "SAMTOOLS CRAM Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + ] + ], + "1": [ + "versions.yml:md5,650a365c6635001436008350ae83337c" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + ] + ], + "versions": [ + "versions.yml:md5,650a365c6635001436008350ae83337c" + ] + } + ], + "timestamp": "2023-12-04T11:07:50.356233402" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml new file mode 100644 index 0000000..7c28e30 --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/stats: + - modules/nf-core/samtools/stats/** diff --git a/modules/nf-core/trimmomatic/environment.yml b/modules/nf-core/trimmomatic/environment.yml new file mode 100644 index 0000000..91145bb --- /dev/null +++ b/modules/nf-core/trimmomatic/environment.yml @@ -0,0 +1,7 @@ +name: trimmomatic +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::trimmomatic=0.39 diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 48d8f18..31f7ffd 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -2,7 +2,7 @@ process TRIMMOMATIC { tag "$meta.id" label 'process_medium' - conda "bioconda::trimmomatic=0.39" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trimmomatic:0.39--hdfd78af_2': 'biocontainers/trimmomatic:0.39--hdfd78af_2' }" diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml index 0a6b18b..0486e9f 100644 --- a/modules/nf-core/trimmomatic/meta.yml +++ b/modules/nf-core/trimmomatic/meta.yml @@ -4,16 +4,13 @@ keywords: - trimming - adapter trimming - quality trimming - tools: - "trimmomatic": description: "A flexible read trimming tool for Illumina NGS data" homepage: "http://www.usadellab.org/cms/?page=trimmomatic" documentation: "https://github.com/usadellab/Trimmomatic" - doi: "10.1093/bioinformatics/btu170" licence: "['GPL v3']" - input: - meta: type: map @@ -25,7 +22,6 @@ input: description: | Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively. pattern: "*.fastq.gz" - output: - meta: type: map @@ -52,6 +48,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@alyssa-ab" +maintainers: + - "@alyssa-ab" diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test b/modules/nf-core/trimmomatic/tests/main.nf.test new file mode 100644 index 0000000..fd855f2 --- /dev/null +++ b/modules/nf-core/trimmomatic/tests/main.nf.test @@ -0,0 +1,95 @@ +nextflow_process { + + name "Test Process TRIMMOMATIC" + script "../main.nf" + process "TRIMMOMATIC" + tag "modules" + tag "modules_nfcore" + tag "trimmomatic" + + test("Single-Read") { + config "./nextflow_SE.config" + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.trimmed_reads != null }, + { assert process.out.trimmed_reads.get(0).get(1) ==~ ".*.SE.paired.trim.fastq.gz" }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Paired-Reads") { + config "./nextflow_PE.config" + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:false ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.trimmed_reads != null }, + { assert process.out.trimmed_reads.get(0).get(1).get(0) ==~ ".*.paired.trim_1.fastq.gz" }, + { assert process.out.trimmed_reads.get(0).get(1).get(1) ==~ ".*.paired.trim_2.fastq.gz" }, + { assert snapshot(process.out).match() }, + { assert snapshot(process.out.versions).match("versions") }, + ) + } + } + + test("No Adaptors") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:false ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.failed } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test.snap b/modules/nf-core/trimmomatic/tests/main.nf.test.snap new file mode 100644 index 0000000..f1519f0 --- /dev/null +++ b/modules/nf-core/trimmomatic/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14413a048f088a147fb04f3d59c6c604" + ] + ], + "timestamp": "2023-10-18T12:15:39.464478" + }, + "Single-Read": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.SE.paired.trim.fastq.gz:md5,089a57f61d7197566b8a3ce71df79113" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.log:md5,e4c3f619e9b0e26847f8f3e3d9af319b" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary:md5,24c973237557a1439c775ca19a5deaa5" + ] + ], + "4": [ + "versions.yml:md5,14413a048f088a147fb04f3d59c6c604" + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.log:md5,e4c3f619e9b0e26847f8f3e3d9af319b" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary:md5,24c973237557a1439c775ca19a5deaa5" + ] + ], + "trimmed_reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.SE.paired.trim.fastq.gz:md5,089a57f61d7197566b8a3ce71df79113" + ] + ], + "unpaired_reads": [ + + ], + "versions": [ + "versions.yml:md5,14413a048f088a147fb04f3d59c6c604" + ] + } + ], + "timestamp": "2023-10-18T12:15:39.471788" + }, + "Paired-Reads": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.paired.trim_1.fastq.gz:md5,575355b98cb5ef9071fad8014c702f4a", + "test.paired.trim_2.fastq.gz:md5,73fb54874d01b2854640266d12cc534a" + ] + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.unpaired.trim_1.fastq.gz:md5,2f7b5a15cc4e73a6fb4af1fa01f575cd", + "test.unpaired.trim_2.fastq.gz:md5,096ad7f876b6b704ef7f9f2c5af3cf74" + ] + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,9629761761a34576b3484bf4174f681f" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.summary:md5,9698e5e5c060bbe64588998fe35f8d71" + ] + ], + "4": [ + "versions.yml:md5,14413a048f088a147fb04f3d59c6c604" + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,9629761761a34576b3484bf4174f681f" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.summary:md5,9698e5e5c060bbe64588998fe35f8d71" + ] + ], + "trimmed_reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.paired.trim_1.fastq.gz:md5,575355b98cb5ef9071fad8014c702f4a", + "test.paired.trim_2.fastq.gz:md5,73fb54874d01b2854640266d12cc534a" + ] + ] + ], + "unpaired_reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.unpaired.trim_1.fastq.gz:md5,2f7b5a15cc4e73a6fb4af1fa01f575cd", + "test.unpaired.trim_2.fastq.gz:md5,096ad7f876b6b704ef7f9f2c5af3cf74" + ] + ] + ], + "versions": [ + "versions.yml:md5,14413a048f088a147fb04f3d59c6c604" + ] + } + ], + "timestamp": "2023-10-18T12:15:44.677305" + } +} \ No newline at end of file diff --git a/modules/nf-core/trimmomatic/tests/nextflow_PE.config b/modules/nf-core/trimmomatic/tests/nextflow_PE.config new file mode 100644 index 0000000..3f8fdfe --- /dev/null +++ b/modules/nf-core/trimmomatic/tests/nextflow_PE.config @@ -0,0 +1,6 @@ +process { + + withName: TRIMMOMATIC { + ext.args = 'ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36' + } +} diff --git a/modules/nf-core/trimmomatic/tests/nextflow_SE.config b/modules/nf-core/trimmomatic/tests/nextflow_SE.config new file mode 100644 index 0000000..af777fd --- /dev/null +++ b/modules/nf-core/trimmomatic/tests/nextflow_SE.config @@ -0,0 +1,6 @@ +process { + + withName: TRIMMOMATIC { + ext.args = 'ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36' + } +} diff --git a/modules/nf-core/trimmomatic/tests/tags.yml b/modules/nf-core/trimmomatic/tests/tags.yml new file mode 100644 index 0000000..68c5af6 --- /dev/null +++ b/modules/nf-core/trimmomatic/tests/tags.yml @@ -0,0 +1,2 @@ +trimmomatic: + - modules/nf-core/trimmomatic/** diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml new file mode 100644 index 0000000..0c9cbb1 --- /dev/null +++ b/modules/nf-core/untar/environment.yml @@ -0,0 +1,11 @@ +name: untar + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.7 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 61461c3..8a75bb9 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index db241a6..a9a2110 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -39,3 +39,8 @@ authors: - "@drpatelh" - "@matthdsm" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test new file mode 100644 index 0000000..679e83c --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test @@ -0,0 +1,55 @@ +nextflow_process { + + name "Test Process UNTAR" + script "../main.nf" + process "UNTAR" + + tag "modules" + tag "modules_nfcore" + tag "untar" + + test("test_untar") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar") }, + ) + } + + } + + test("test_untar_onlyfiles") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + ) + } + + } + +} diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap new file mode 100644 index 0000000..ace4257 --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -0,0 +1,34 @@ +{ + "test_untar_onlyfiles": { + "content": [ + [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ] + ], + "timestamp": "2023-10-18T11:56:46.878844" + }, + "test_untar": { + "content": [ + [ + [ + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ] + ], + "timestamp": "2023-10-18T11:56:08.16574" + } +} \ No newline at end of file diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml new file mode 100644 index 0000000..feb6f15 --- /dev/null +++ b/modules/nf-core/untar/tests/tags.yml @@ -0,0 +1,2 @@ +untar: + - modules/nf-core/untar/** diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf index 6e3df33..de8130f 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -26,13 +26,9 @@ workflow BAM_MARKDUPLICATES_PICARD { ch_bam_bai = PICARD_MARKDUPLICATES.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) - .map { - meta, bam, bai, csi -> - if (bai) { - [ meta, bam, bai ] - } else { - [ meta, bam, csi ] - } + .map{meta, bam, bai, csi -> + if (bai) [ meta, bam, bai ] + else [ meta, bam, csi ] } BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml index b924596..fe63068 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml +++ b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml @@ -6,7 +6,6 @@ keywords: - bam - sam - cram - components: - picard/markduplicates - samtools/index @@ -14,7 +13,6 @@ components: - samtools/idxstats - samtools/flagstat - bam_stats_samtools - input: - ch_bam: description: | @@ -60,3 +58,6 @@ output: authors: - "@dmarron" - "@drpatelh" +maintainers: + - "@dmarron" + - "@drpatelh" diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test new file mode 100644 index 0000000..d8d2429 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -0,0 +1,93 @@ +nextflow_workflow { + + name "Test Workflow BAM_MARKDUPLICATES_PICARD" + script "../main.nf" + workflow "BAM_MARKDUPLICATES_PICARD" + + tag "picard" + tag "picard/markduplicates" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_markduplicates_picard" + tag "subworkflows/bam_markduplicates_picard" + tag "subworkflows/bam_stats_samtools" + tag "bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/index" + tag "samtools/stats" + + test("sarscov2 - bam") { + + when { + workflow { + """ + 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) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + path(workflow.out.bam[0][1]), + path(workflow.out.bai[0][1]), + path(workflow.out.flagstat[0][1]), + path(workflow.out.idxstats[0][1]), + path(workflow.out.stats[0][1]), + ).match("sarscov2 - bam") }, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("97") } + ) + } + } + + test("homo_sapiens - cram") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + path(workflow.out.bam[0][1]), + path(workflow.out.bai[0][1]), + path(workflow.out.flagstat[0][1]), + path(workflow.out.idxstats[0][1]), + path(workflow.out.stats[0][1]), + ).match("homo_sapiens - cram") }, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("0.999986") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap new file mode 100644 index 0000000..a208d10 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "homo_sapiens - cram": { + "content": [ + "test.bam:md5,6641dc05efa8384a061f378d86d922cd", + "test.bam.bai:md5,c41c60d8a94adebe53b6df80b6e90d38", + "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", + "test.stats:md5,0035ac8900d85e9a790f4c1f48b76947" + ], + "timestamp": "2023-12-05T17:45:12.484869" + }, + "sarscov2 - bam": { + "content": [ + "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", + "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", + "test.stats:md5,e32e7e49dce1fbe327a89e0fb7bc01b1" + ], + "timestamp": "2023-12-05T17:43:58.582652" + } +} diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml new file mode 100644 index 0000000..10b8527 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_markduplicates_picard: + - subworkflows/nf-core/bam_markduplicates_picard/** diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml index 87863b1..809bf73 100644 --- a/subworkflows/nf-core/bam_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -39,3 +39,5 @@ output: Structure: [ path(versions.yml) ] authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test new file mode 100644 index 0000000..c8b21f2 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_workflow { + + name "Test Workflow BAM_STATS_SAMTOOLS" + script "../main.nf" + workflow "BAM_STATS_SAMTOOLS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_stats_samtools" + tag "subworkflows/bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/stats" + + test("test_bam_stats_samtools_single_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end_cram") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap new file mode 100644 index 0000000..8bf0d37 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -0,0 +1,128 @@ +{ + "test_bam_stats_samtools_paired_end_cram_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + ] + ] + ], + "timestamp": "2023-11-06T09:31:26.194017574" + }, + "test_bam_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,49e2b43344ff92bc4c02463a58f7ba4a" + ] + ] + ], + "timestamp": "2024-01-18T17:17:27.704335" + }, + "test_bam_stats_samtools_paired_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "timestamp": "2024-01-18T17:17:27.717482" + }, + "test_bam_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "timestamp": "2023-11-06T09:26:10.340046381" + }, + "test_bam_stats_samtools_paired_end_cram_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" + ] + ] + ], + "timestamp": "2023-11-06T09:31:26.207052003" + }, + "test_bam_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,5a6667d97806e5002731e9cf23674fad" + ] + ] + ], + "timestamp": "2023-12-04T11:07:06.676820877" + }, + "test_bam_stats_samtools_paired_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2024-01-18T17:17:27.726719" + }, + "test_bam_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "timestamp": "2023-11-06T09:26:10.349439801" + }, + "test_bam_stats_samtools_paired_end_cram_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,2cf2fe93596ee3d74f946097b204a629" + ] + ] + ], + "timestamp": "2023-12-04T11:07:22.30295557" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml new file mode 100644 index 0000000..ec2f2d6 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_stats_samtools: + - subworkflows/nf-core/bam_stats_samtools/** diff --git a/subworkflows/nf-core/fastq_align_bwaaln/meta.yml b/subworkflows/nf-core/fastq_align_bwaaln/meta.yml index ad43398..5ba4665 100644 --- a/subworkflows/nf-core/fastq_align_bwaaln/meta.yml +++ b/subworkflows/nf-core/fastq_align_bwaaln/meta.yml @@ -26,7 +26,6 @@ input: Structure: [ val(meta), path(index) ] A directory containing bwa aln reference indices as from `bwa index` Contains files ending in extensions such as .amb, .ann, .bwt etc. - output: - bam: description: | @@ -49,3 +48,5 @@ output: Structure: [ path(versions.yml) ] authors: - "@jfy133" +maintainers: + - "@jfy133"
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow
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