nf-core_modules/modules/ichorcna/run/main.nf

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def VERSION = '0.3.2' // Version information not provided by tool on CLI
process ICHORCNA_RUN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }"
input:
tuple val(meta), path(wig)
path gc_wig
path map_wig
path panel_of_normals
path centromere
output:
tuple val(meta), path("*.cna.seg") , emit: cna_seg
tuple val(meta), path("*.params.txt") , emit: ichorcna_params
path "**/*genomeWide.pdf" , emit: genome_plot
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}"
def pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : ''
def centro = centromere ? "--centromere ${centromere}" : ''
"""
runIchorCNA.R --id ${prefix} \\
$args \\
--WIG ${wig} \\
--id ${meta.id} \\
--gcWig ${gc_wig} \\
--mapWig ${map_wig} \\
${pon} \\
${centro} \\
--outDir .
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ichorcna: $VERSION
END_VERSIONS
"""
}