nf-core_modules/modules/deeptools/bamcoverage/main.nf
2022-03-24 19:44:31 +00:00

37 lines
1.1 KiB
Text

process DEEPTOOLS_BAMCOVERAGE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
input:
tuple val(meta), path(input), path(input_index)
output:
tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true
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}.bigWig"
"""
bamCoverage \\
--bam $input \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
END_VERSIONS
"""
}