diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml index ad1ff8498d0b..fbe5608cce9c 100644 --- a/modules/nf-core/strelka/germline/environment.yml +++ b/modules/nf-core/strelka/germline/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python=2.7.15 - bioconda::strelka=2.9.10=h9ee0642_1 + - conda-forge::python=2.7.15 diff --git a/modules/nf-core/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf index b528d3dd3ad8..67e2680fd0df 100644 --- a/modules/nf-core/strelka/germline/main.nf +++ b/modules/nf-core/strelka/germline/main.nf @@ -18,7 +18,7 @@ process STRELKA_GERMLINE { tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi tuple val(meta), path("*genome.vcf.gz"), emit: genome_vcf tuple val(meta), path("*genome.vcf.gz.tbi"), emit: genome_vcf_tbi - path "versions.yml", emit: versions + tuple val("${task.process}"), val('strelka'), eval("configureStrelkaGermlineWorkflow.py --version"), emit: versions_strelka, topic: versions when: task.ext.when == null || task.ext.when @@ -42,11 +42,6 @@ process STRELKA_GERMLINE { mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - strelka: \$( configureStrelkaGermlineWorkflow.py --version ) - END_VERSIONS """ stub: @@ -56,10 +51,5 @@ process STRELKA_GERMLINE { touch ${prefix}.genome.vcf.gz.tbi echo "" | gzip > ${prefix}.variants.vcf.gz touch ${prefix}.variants.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - strelka: \$( configureStrelkaSomaticWorkflow.py --version ) - END_VERSIONS """ } diff --git a/modules/nf-core/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml index c20bf89a6a15..4150d974b1b6 100644 --- a/modules/nf-core/strelka/germline/meta.yml +++ b/modules/nf-core/strelka/germline/meta.yml @@ -1,6 +1,6 @@ name: strelka_germline -description: Strelka2 is a fast and accurate small variant caller optimized for analysis - of germline variation +description: Strelka2 is a fast and accurate small variant caller optimized for + analysis of germline variation keywords: - variantcalling - germline @@ -9,13 +9,14 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing - reads + description: Strelka calls somatic and germline small variants from mapped + sequencing reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:strelka input: - - meta: @@ -40,7 +41,8 @@ input: ontologies: [] - target_bed_index: type: file - description: Index for BED file containing target regions for variant calling + description: Index for BED file containing target regions for variant + calling pattern: "*.{bed.tbi}" ontologies: [] - fasta: @@ -99,13 +101,29 @@ output: description: index file for the genome_vcf file pattern: "*_genome.vcf.gz.tbi" ontologies: [] + versions_strelka: + - - ${task.process}: + type: string + description: The name of the process + - strelka: + type: string + description: The name of the tool + - configureStrelkaGermlineWorkflow.py --version: + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - strelka: + type: string + description: The name of the tool + - configureStrelkaGermlineWorkflow.py --version: + type: eval + description: The expression to obtain the version of the tool + authors: - "@arontommi" maintainers: diff --git a/modules/nf-core/strelka/germline/tests/main.nf.test b/modules/nf-core/strelka/germline/tests/main.nf.test index 6d93a6c84e8d..a43ff2d435be 100644 --- a/modules/nf-core/strelka/germline/tests/main.nf.test +++ b/modules/nf-core/strelka/germline/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { process.out.vcf_tbi.collect { file(it[1]).getName() }, path(process.out.genome_vcf.get(0).get(1)).vcf.variantsMD5, process.out.genome_vcf_tbi.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -70,7 +70,7 @@ nextflow_process { process.out.vcf_tbi.collect { file(it[1]).getName() }, path(process.out.genome_vcf.get(0).get(1)).vcf.variantsMD5, process.out.genome_vcf_tbi.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -98,7 +98,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/strelka/germline/tests/main.nf.test.snap b/modules/nf-core/strelka/germline/tests/main.nf.test.snap index 174ce79a149e..9db6dda7a2d2 100644 --- a/modules/nf-core/strelka/germline/tests/main.nf.test.snap +++ b/modules/nf-core/strelka/germline/tests/main.nf.test.snap @@ -2,41 +2,6 @@ "human - cram - stub": { "content": [ { - "0": [ - [ - { - "id": "test" - }, - "test.variants.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.variants.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "test.genome.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "test.genome.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65" - ], "genome_vcf": [ [ { @@ -69,16 +34,20 @@ "test.variants.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65" + "versions_strelka": [ + [ + "STRELKA_GERMLINE", + "strelka", + "2.9.10" + ] ] } ], + "timestamp": "2026-07-08T08:53:23.28237163", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-20T16:07:30.81195" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human - cram": { "content": [ @@ -90,15 +59,21 @@ [ "test.genome.vcf.gz.tbi" ], - [ - "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65" - ] + { + "versions_strelka": [ + [ + "STRELKA_GERMLINE", + "strelka", + "2.9.10" + ] + ] + } ], + "timestamp": "2026-07-08T08:52:36.087466651", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" - }, - "timestamp": "2025-09-29T15:09:16.999086" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human - cram - target": { "content": [ @@ -110,14 +85,20 @@ [ "test.genome.vcf.gz.tbi" ], - [ - "versions.yml:md5,5f72393fd2ab4358e3f0ad16d1937f65" - ] + { + "versions_strelka": [ + [ + "STRELKA_GERMLINE", + "strelka", + "2.9.10" + ] + ] + } ], + "timestamp": "2026-07-08T08:53:17.021875762", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" - }, - "timestamp": "2025-09-29T15:10:22.364952" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml index ad1ff8498d0b..fbe5608cce9c 100644 --- a/modules/nf-core/strelka/somatic/environment.yml +++ b/modules/nf-core/strelka/somatic/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python=2.7.15 - bioconda::strelka=2.9.10=h9ee0642_1 + - conda-forge::python=2.7.15 diff --git a/modules/nf-core/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf index b98535cc8c49..8b296755722c 100644 --- a/modules/nf-core/strelka/somatic/main.nf +++ b/modules/nf-core/strelka/somatic/main.nf @@ -18,7 +18,7 @@ process STRELKA_SOMATIC { tuple val(meta), path("*.somatic_indels.vcf.gz.tbi"), emit: vcf_indels_tbi tuple val(meta), path("*.somatic_snvs.vcf.gz"), emit: vcf_snvs tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi"), emit: vcf_snvs_tbi - path "versions.yml", emit: versions + tuple val("${task.process}"), val('strelka'), eval("configureStrelkaSomaticWorkflow.py --version"), emit: versions_strelka, topic: versions when: task.ext.when == null || task.ext.when @@ -45,11 +45,6 @@ process STRELKA_SOMATIC { mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}.somatic_indels.vcf.gz.tbi mv strelka/results/variants/somatic.snvs.vcf.gz ${prefix}.somatic_snvs.vcf.gz mv strelka/results/variants/somatic.snvs.vcf.gz.tbi ${prefix}.somatic_snvs.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - strelka: \$( configureStrelkaSomaticWorkflow.py --version ) - END_VERSIONS """ stub: @@ -59,10 +54,6 @@ process STRELKA_SOMATIC { touch ${prefix}.somatic_indels.vcf.gz.tbi echo "" | gzip > ${prefix}.somatic_snvs.vcf.gz touch ${prefix}.somatic_snvs.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - strelka: \$( configureStrelkaSomaticWorkflow.py --version ) - END_VERSIONS """ } +} diff --git a/modules/nf-core/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml index eca9ea43f265..aeb3a8080ab4 100644 --- a/modules/nf-core/strelka/somatic/meta.yml +++ b/modules/nf-core/strelka/somatic/meta.yml @@ -1,7 +1,7 @@ name: strelka_somatic -description: Strelka2 is a fast and accurate small variant caller optimized for analysis - of germline variation in small cohorts and somatic variation in tumor/normal sample - pairs +description: Strelka2 is a fast and accurate small variant caller optimized for + analysis of germline variation in small cohorts and somatic variation in + tumor/normal sample pairs keywords: - variant calling - germline @@ -10,13 +10,14 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing - reads + description: Strelka calls somatic and germline small variants from mapped + sequencing reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:strelka input: - - meta: @@ -61,7 +62,8 @@ input: ontologies: [] - target_bed_index: type: file - description: Index for BED file containing target regions for variant calling + description: Index for BED file containing target regions for variant + calling pattern: "*.{bed.tbi}" ontologies: [] - fasta: @@ -119,13 +121,29 @@ output: description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" ontologies: [] + versions_strelka: + - - ${task.process}: + type: string + description: The name of the process + - strelka: + type: string + description: The name of the tool + - configureStrelkaSomaticWorkflow.py --version: + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - strelka: + type: string + description: The name of the tool + - configureStrelkaSomaticWorkflow.py --version: + type: eval + description: The expression to obtain the version of the tool + authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/strelka/somatic/tests/main.nf.test b/modules/nf-core/strelka/somatic/tests/main.nf.test index 89cc9efa2034..5118b6c29701 100644 --- a/modules/nf-core/strelka/somatic/tests/main.nf.test +++ b/modules/nf-core/strelka/somatic/tests/main.nf.test @@ -37,7 +37,7 @@ nextflow_process { process.out.vcf_indels_tbi.collect { file(it[1]).getName() }, path(process.out.vcf_snvs.get(0).get(1)).vcf.variantsMD5, process.out.vcf_snvs_tbi.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -72,7 +72,7 @@ nextflow_process { process.out.vcf_indels_tbi.collect { file(it[1]).getName() }, path(process.out.vcf_snvs.get(0).get(1)).vcf.variantsMD5, process.out.vcf_snvs_tbi.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -113,7 +113,7 @@ nextflow_process { process.out.vcf_indels_tbi.collect { file(it[1]).getName() }, path(process.out.vcf_snvs.get(0).get(1)).vcf.variantsMD5, process.out.vcf_snvs_tbi.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -145,7 +145,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } diff --git a/modules/nf-core/strelka/somatic/tests/main.nf.test.snap b/modules/nf-core/strelka/somatic/tests/main.nf.test.snap index 5336e31a4d28..18d91e24ffc2 100644 --- a/modules/nf-core/strelka/somatic/tests/main.nf.test.snap +++ b/modules/nf-core/strelka/somatic/tests/main.nf.test.snap @@ -9,58 +9,25 @@ [ "test.somatic_snvs.vcf.gz.tbi" ], - [ - "versions.yml:md5,97860fb8f9cda9494819160f7cf6e35b" - ] + { + "versions_strelka": [ + [ + "STRELKA_SOMATIC", + "strelka", + "2.9.10" + ] + ] + } ], + "timestamp": "2026-07-08T08:55:26.02055306", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-04-08T14:18:48.400058" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human - cram - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.somatic_indels.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.somatic_indels.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.somatic_snvs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.somatic_snvs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,97860fb8f9cda9494819160f7cf6e35b" - ], "vcf_indels": [ [ { @@ -97,16 +64,20 @@ "test.somatic_snvs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,97860fb8f9cda9494819160f7cf6e35b" + "versions_strelka": [ + [ + "STRELKA_SOMATIC", + "strelka", + "2.9.10" + ] ] } ], + "timestamp": "2026-07-08T08:55:32.347412341", "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-20T15:08:42.361540303" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human - cram": { "content": [ @@ -118,15 +89,21 @@ [ "test.somatic_snvs.vcf.gz.tbi" ], - [ - "versions.yml:md5,97860fb8f9cda9494819160f7cf6e35b" - ] + { + "versions_strelka": [ + [ + "STRELKA_SOMATIC", + "strelka", + "2.9.10" + ] + ] + } ], + "timestamp": "2026-07-08T08:54:02.863317401", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-04-08T14:17:42.760334" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "human - bam": { "content": [ @@ -138,14 +115,20 @@ [ "test.somatic_snvs.vcf.gz.tbi" ], - [ - "versions.yml:md5,97860fb8f9cda9494819160f7cf6e35b" - ] + { + "versions_strelka": [ + [ + "STRELKA_SOMATIC", + "strelka", + "2.9.10" + ] + ] + } ], + "timestamp": "2026-07-08T08:54:46.067226446", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" - }, - "timestamp": "2025-04-08T14:48:34.656324" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file