mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
49 lines
1.7 KiB
Text
49 lines
1.7 KiB
Text
process ICHORCNA_RUN {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
|
|
container "${ 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}" : ''
|
|
def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
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
|
|
"""
|
|
}
|