nf-core_modules/modules/plink2/extract/main.nf
Benjamin Wingfield e687c7025a
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>
2022-02-03 10:42:56 +00:00

37 lines
1.3 KiB
Text

process PLINK2_EXTRACT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
input:
tuple val(meta), path(pgen), path(psam), path(pvar), path(variants)
output:
tuple val(meta), path("*.pgen") , emit: extract_pgen
tuple val(meta), path("*.psam") , emit: extract_psam
tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
"""
plink2 \\
--pfile ${pgen.baseName} \\
$args \\
--threads $task.cpus \\
--extract $variants \\
--make-pgen vzs \\
--out ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
END_VERSIONS
"""
}