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mkatsantoMaria KatsantonifamosabSPPearce
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feat: addition of vembrane table module (#9285)
* fix: linting error * fix: add conda snapshot * fix: test path specification and removed test prefix * fix: add explicit version displayed * fix: revert the snapshot syntax * fix: explicit version snapshot retry * fix: remove newline * Update modules/nf-core/vembrane/table/tests/main.nf.test Co-authored-by: Famke Bäuerle <[email protected]> * Apply suggestions from code review Co-authored-by: Famke Bäuerle <[email protected]> * fix: apply formatting code review changes * Update modules/nf-core/vembrane/table/main.nf * Update modules/nf-core/vembrane/table/main.nf --------- Co-authored-by: Maria Katsantoni <[email protected]> Co-authored-by: Famke Bäuerle <[email protected]> Co-authored-by: Simon Pearce <[email protected]>
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‎modules/nf-core/vembrane/table/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::vembrane=2.4.0

‎modules/nf-core/vembrane/table/main.nf‎

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process VEMBRANE_TABLE {
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tag "${meta.id}"
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label 'process_low'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0'
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: 'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
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input:
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tuple val(meta), path(vcf)
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val expression
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output:
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tuple val(meta), path("*.tsv"), emit: table
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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vembrane table \\
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${args} \\
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--output ${prefix}.tsv \\
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'${expression}' \\
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${vcf}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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vembrane: \$(vembrane --version | sed '1!d;s/.* //')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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vembrane: \$(vembrane --version | sed '1!d;s/.* //')
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END_VERSIONS
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"""
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}

‎modules/nf-core/vembrane/table/meta.yml‎

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "vembrane_table"
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description: Creates tabular (TSV) files from VCF/BCF data with flexible Python expressions
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keywords:
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- vcf
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- bcf
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- table
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- genomics
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- variant
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- annotation
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tools:
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- "vembrane":
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description: "Filter VCF/BCF files with Python expressions"
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homepage: "https://vembrane.github.io/"
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documentation: "https://github.com/vembrane/vembrane/blob/main/docs/table.md"
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tool_dev_url: "https://github.com/vembrane/vembrane"
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doi: "10.1093/bioinformatics/btac810"
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licence: ["MIT"]
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identifier: biotools:vembrane
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args_id: "$args"
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- vcf:
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type: file
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description: VCF/BCF file to extract tabular data from
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pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
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ontologies:
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- edam: http://edamontology.org/format_3016 # VCF
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- expression:
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type: string
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description: A comma-separated tuple of expressions that define the table column contents
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output:
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table:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1', single_end:false ]`
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- "*.tsv":
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type: file
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description: TSV file containing tabular data from VCF/BCF
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pattern: "*.tsv"
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ontologies:
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- edam: http://edamontology.org/format_3475 # TSV
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versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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ontologies:
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- edam: http://edamontology.org/format_3750 # YAML
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authors:
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- "@mkatsanto"
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- "@trangdo-hsc"
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maintainers:
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- "@mkatsanto"
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- "@trangdo-hsc"

‎modules/nf-core/vembrane/table/tests/main.nf.test‎

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nextflow_process {
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name "Test Process VEMBRANE_TABLE"
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script "../main.nf"
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process "VEMBRANE_TABLE"
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tag "modules"
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tag "modules_nfcore"
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tag "vembrane"
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tag "vembrane/table"
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test("homo_sapiens - [vcf] - tsv") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
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]
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input[1] = 'CHROM, POS, REF, ALT, QUAL'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - [bcf.gz] - tsv") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
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]
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input[1] = 'CHROM, POS, REF, ALT, QUAL'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - [vcf] - csv - custom_separator") {
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config "./nextflow.config"
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when {
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params {
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vembrane_args = '--separator ,'
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}
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
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]
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input[1] = 'CHROM, POS, REF, ALT'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - [vcf] - tsv - custom_header") {
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config "./nextflow.config"
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when {
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params {
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vembrane_args = '--header "Chromosome,Position,Variant_ID,Quality"'
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}
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
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]
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input[1] = 'CHROM, POS, ID, QUAL'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(process.out).match() }
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)
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}
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}
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test("homo_sapiens - [vcf] - tsv - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ], // meta map
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
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]
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input[1] = 'CHROM, POS, REF, ALT, QUAL'
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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process.out,
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path(process.out.versions[0]).yaml
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).match() }
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)
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}
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}
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}

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