nf-core_modules/modules/cnvkit/batch/main.nf
2022-06-01 17:35:02 +02:00

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process CNVKIT_BATCH {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' :
'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-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
tuple val(meta), path("*.pdf"), emit: pdf, optional: true
tuple val(meta), path("*.png"), emit: png, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def tumor_exists = tumor ? true : false
def normal_exists = normal ? true : false
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
// tumor_only mode does not need fasta & target
// instead it requires a pre-computed reference.cnn which is built from fasta & target
def (normal_out, normal_args, fasta_args) = ["", "", ""]
if (normal_exists){
def normal_prefix = normal.BaseName
normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
fasta_args = fasta ? "--fasta $fasta" : ""
// germline mode
// normal samples must be input without a flag
// requires flag --normal to be empty
if(!tumor_exists){
tumor_out = normal.BaseName + ".bam"
normal_args = "--normal "
}
// somatic mode
else {
normal_args = normal_prefix ? "--normal $normal_out" : ""
}
}
def target_args = targets ? "--targets $targets" : ""
def reference_args = reference ? "--reference $reference" : ""
"""
if $tumor_cram; then
samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
fi
if $normal_cram; then
samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
fi
cnvkit.py \\
batch \\
$tumor_out \\
$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
"""
}