nf-core_modules/modules/bamcmp/main.nf

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def VERSION = '2.2'
process BAMCMP {
label 'process_low'
conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"
input:
tuple val(meta), path(sample), path(contaminant)
output:
tuple val(meta), path("*primary.bam") , emit: bam
tuple val(meta), path("*contamination.bam"), emit: contamination_bam
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bamcmp \\
-1 $sample \\
-2 $contaminant \\
-A ${prefix}_primary.bam \\
-B ${prefix}_contamination.bam \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamcmp: $VERSION
END_VERSIONS
"""
}