New module: `plink2/extract` (#1228)
* add plink2_extract * fix test yml path * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * compress output * add DOI * make outputs less ambiguous * update test for compressed output * brain is dumb * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>bat-test
Benjamin Wingfield
2 years ago
committed by
GitHub
parent
f112e4d701
commit
e687c7025a
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process PLINK2_EXTRACT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
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'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
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input:
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tuple val(meta), path(pgen), path(psam), path(pvar), path(variants)
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output:
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tuple val(meta), path("*.pgen") , emit: extract_pgen
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tuple val(meta), path("*.psam") , emit: extract_psam
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tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
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"""
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plink2 \\
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--pfile ${pgen.baseName} \\
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$args \\
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--threads $task.cpus \\
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--extract $variants \\
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--make-pgen vzs \\
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--out ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
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END_VERSIONS
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"""
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}
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name: plink2_extract
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description: Subset plink pfiles with a text file of variant identifiers
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keywords:
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- plink2
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- extract
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tools:
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- plink2:
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description: |
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Whole genome association analysis toolset, designed to perform a range
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of basic, large-scale analyses in a computationally efficient manner
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homepage: http://www.cog-genomics.org/plink/2.0/
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documentation: http://www.cog-genomics.org/plink/2.0/general_usage
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tool_dev_url: None
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doi: "10.1186/s13742-015-0047-8"
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licence: ['GPL v3']
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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:'test', single_end:false ]
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- pgen:
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type: file
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description: PLINK 2 binary genotype table
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pattern: "*.{pgen}"
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- psam:
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type: file
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description: PLINK 2 sample information file
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pattern: "*.{psam}"
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- pvar:
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type: file
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description: PLINK 2 variant information file
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pattern: "*.{pvar}"
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- variants:
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type: file
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description: A text file containing variant identifiers to keep (one per line)
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pattern: "*.{keep}"
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output:
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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:'test', single_end:false ]
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- versions:
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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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- extract_pgen:
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type: file
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description: PLINK 2 binary genotype table, containing extracted variants
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pattern: "*.{pgen}"
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- extract_psam:
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type: file
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description: PLINK 2 sample information file associated with the extracted data
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pattern: "*.{psam}"
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- extract_pvar:
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type: file
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description: PLINK 2 variant information file, containing extracted variants
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pattern: "*.{pvar.zst}"
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authors:
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- "@nebfield"
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@ -0,0 +1,30 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
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include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf'
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workflow test_plink2_extract {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
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]
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PLINK2_VCF ( input )
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PLINK2_VCF.out.pvar
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.splitText(file: 'variants.keep', keepHeader: false, by: 10)
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.last()
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.set { ch_variants }
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ch_variants.view()
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PLINK2_VCF.out.pgen
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.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.concat(ch_variants))
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.groupTuple()
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.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
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.set { ch_extract }
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PLINK2_EXTRACT ( ch_extract )
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}
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@ -0,0 +1,12 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: PLINK2_VCF {
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ext.args = '--make-pgen --set-missing-var-ids @:#:\\$1:\\$2'
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}
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withName: PLINK2_EXTRACT {
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ext.prefix = { "${meta.id}.extract" }
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}
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}
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@ -0,0 +1,20 @@
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- name: plink2 extract test_plink2_extract
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command: nextflow run tests/modules/plink2/extract -entry test_plink2_extract -c tests/config/nextflow.config
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tags:
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- plink2/extract
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- plink2
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files:
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- path: output/plink2/test.extract.pgen
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md5sum: 785e729a293ecabb0d39394865316bda
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- path: output/plink2/test.extract.psam
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md5sum: e6c714488754cb8448c3dfda08c4c0ea
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- path: output/plink2/test.extract.pvar.zst
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md5sum: 076767e6695e681115eabb924a447ee9
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- path: output/plink2/test.pgen
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md5sum: fac12ca9041d6950f6b7d60ac2120721
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- path: output/plink2/test.psam
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md5sum: e6c714488754cb8448c3dfda08c4c0ea
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- path: output/plink2/test.pvar
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md5sum: ff9e44f8e5f4035d8cf2bfe7be6755b3
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- path: output/plink2/versions.yml
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md5sum: c477b7c9f6e39b89710fe1a0bceee50d
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