mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
55 lines
1.6 KiB
Text
55 lines
1.6 KiB
Text
process CNVKIT_BATCH {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' :
|
|
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(tumor), path(normal)
|
|
path fasta
|
|
path targets
|
|
path reference
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed"), emit: bed
|
|
tuple val(meta), path("*.cnn"), emit: cnn, optional: true
|
|
tuple val(meta), path("*.cnr"), emit: cnr, optional: true
|
|
tuple val(meta), path("*.cns"), emit: cns, optional: true
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def normal_args = normal ? "--normal $normal" : ""
|
|
def fasta_args = fasta ? "--fasta $fasta" : ""
|
|
def reference_args = reference ? "--reference $reference" : ""
|
|
|
|
def target_args = ""
|
|
if (args.contains("--method wgs") || args.contains("-m wgs")) {
|
|
target_args = targets ? "--targets $targets" : ""
|
|
}
|
|
else {
|
|
target_args = "--targets $targets"
|
|
}
|
|
"""
|
|
cnvkit.py \\
|
|
batch \\
|
|
$tumor \\
|
|
$normal_args \\
|
|
$fasta_args \\
|
|
$reference_args \\
|
|
$target_args \\
|
|
--processes $task.cpus \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|