diff --git a/modules/nf-core/octopusv/correct/environment.yml b/modules/nf-core/octopusv/correct/environment.yml new file mode 100644 index 00000000000..583655a9621 --- /dev/null +++ b/modules/nf-core/octopusv/correct/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::octopusv=0.3.2" diff --git a/modules/nf-core/octopusv/correct/main.nf b/modules/nf-core/octopusv/correct/main.nf new file mode 100644 index 00000000000..db05cf42832 --- /dev/null +++ b/modules/nf-core/octopusv/correct/main.nf @@ -0,0 +1,46 @@ +process OCTOPUSV_CORRECT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/octopusv:0.3.2--pyhdfd78af_0' : + 'quay.io/biocontainers/octopusv:0.3.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.svcf"), emit: svcf + tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + vcf_in="${vcf}" + if [[ "${vcf}" == *.gz ]]; then + gunzip -c ${vcf} > ${prefix}.input.vcf + vcf_in="${prefix}.input.vcf" + fi + + octopusv correct \\ + -i \${vcf_in} \\ + -o ${prefix}.svcf \\ + $args + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo $args + + touch ${prefix}.svcf + """ +} diff --git a/modules/nf-core/octopusv/correct/meta.yml b/modules/nf-core/octopusv/correct/meta.yml new file mode 100644 index 00000000000..ec980e5b437 --- /dev/null +++ b/modules/nf-core/octopusv/correct/meta.yml @@ -0,0 +1,68 @@ +name: "octopusv_correct" +description: "Standardize a caller VCF into OctopuSV SVCF format." +keywords: + - structural + - variant + - sv + - svcf + - normalize +tools: + - "octopusv": + description: "End-to-end structural variant post-processing: standardize, merge, + compare, and export SVs." + homepage: "https://github.com/ylab-hi/OctopuSV" + documentation: "https://github.com/ylab-hi/OctopuSV" + tool_dev_url: "https://github.com/ylab-hi/OctopuSV" + doi: "10.1093/bioinformatics/btaf599" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - vcf: + type: file + description: Structural variant calls in VCF format + pattern: "*.{vcf,vcf.gz}" + ontologies: + - edam: "http://edamontology.org/format_3016" # VCF +output: + svcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + - "*.svcf": + type: file + description: Standardized SVCF file + pattern: "*.svcf" + ontologies: + - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF + versions_octopusv: + - - ${task.process}: + type: string + description: The name of the process + - octopusv: + type: string + description: The name of the tool + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - octopusv: + type: string + description: The name of the tool + - python -c "import importlib.metadata as m; print(m.version('octopusv'))": + type: eval + description: The expression to obtain the version of the tool +authors: + - "@manascripts" +maintainers: + - "@manascripts" diff --git a/modules/nf-core/octopusv/correct/tests/main.nf.test b/modules/nf-core/octopusv/correct/tests/main.nf.test new file mode 100644 index 00000000000..f64d6f9ef4c --- /dev/null +++ b/modules/nf-core/octopusv/correct/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process OCTOPUSV_CORRECT" + script "../main.nf" + process "OCTOPUSV_CORRECT" + + tag "modules" + tag "modules_nfcore" + tag "octopusv" + tag "octopusv/correct" + + test("homo_sapiens - vcf.gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.svcf.get(0).get(1)).vcf.summary, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("homo_sapiens - vcf.gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + + } + +} diff --git a/modules/nf-core/octopusv/correct/tests/main.nf.test.snap b/modules/nf-core/octopusv/correct/tests/main.nf.test.snap new file mode 100644 index 00000000000..9440fe86de1 --- /dev/null +++ b/modules/nf-core/octopusv/correct/tests/main.nf.test.snap @@ -0,0 +1,47 @@ +{ + "homo_sapiens - vcf.gz": { + "content": [ + "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=136, phased=false, phasedAutodetect=false]", + { + "versions_octopusv": [ + [ + "OCTOPUSV_CORRECT", + "octopusv", + "0.3.2" + ] + ] + } + ], + "timestamp": "2026-05-08T17:09:49.514026439", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "homo_sapiens - vcf.gz - stub": { + "content": [ + { + "svcf": [ + [ + { + "id": "test" + }, + "test.svcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_octopusv": [ + [ + "OCTOPUSV_CORRECT", + "octopusv", + "0.3.2" + ] + ] + } + ], + "timestamp": "2026-05-08T17:09:57.951939979", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file