nf-core_modules/modules/ichorcna/createpon/main.nf
2022-06-27 10:35:41 +02:00

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process ICHORCNA_CREATEPON {
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:
path wigs
path gc_wig
path map_wig
path centromere
output:
path "*.rds" , emit: rds
path "*.txt" , emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def centro = centromere ? "--centromere ${centromere}" : ''
def prefix = task.ext.prefix ?: "PoN"
def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
echo ${wigs} | tr " " "\\n" > wig_files.txt
createPanelOfNormals.R \\
--filelist wig_files.txt \\
--gcWig ${gc_wig} \\
--mapWig ${map_wig} \\
${centro} \\
${args} \\
--outfile ${prefix}
rm wig_files.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ichorcna: $VERSION
END_VERSIONS
"""
}