mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
53 lines
1.4 KiB
Text
53 lines
1.4 KiB
Text
process PEDDY {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' :
|
|
'quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(vcf_tbi)
|
|
path ped
|
|
|
|
output:
|
|
tuple val(meta), path("*.html") , emit: html
|
|
tuple val(meta), path("*.csv") , emit: csv
|
|
tuple val(meta), path("*.peddy.ped"), emit: ped
|
|
tuple val(meta), path("*.png") , optional: true, emit: png
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
peddy \\
|
|
$args \\
|
|
--plot \\
|
|
-p $task.cpus \\
|
|
$vcf \\
|
|
$ped
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
|
|
END_VERSIONS
|
|
"""
|
|
|
|
stub:
|
|
"""
|
|
filename=\$(basename $vcf)
|
|
touch \$filename.ped_check.csv
|
|
touch \$filename.vs.html
|
|
touch \$filename.het_check.csv
|
|
touch \$filename.sex_check.csv
|
|
touch \$filename.peddy.ped
|
|
touch \$filename.html
|
|
|
|
touch versions.yml
|
|
"""
|
|
}
|