nf-core_modules/modules/deeptools/plotfingerprint/main.nf

49 lines
1.9 KiB
Text
Raw Normal View History

2020-09-10 15:45:11 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
2020-09-10 15:45:11 +00:00
params.options = [:]
options = initOptions(params.options)
2020-09-10 15:45:11 +00:00
process DEEPTOOLS_PLOTFINGERPRINT {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
2020-09-10 15:45:11 +00:00
conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
2020-12-14 00:05:48 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
2020-12-14 00:05:48 +00:00
} else {
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
2020-12-14 00:05:48 +00:00
}
2020-09-10 15:45:11 +00:00
input:
tuple val(meta), path(bams), path(bais)
2020-12-17 23:50:24 +00:00
2020-09-10 15:45:11 +00:00
output:
tuple val(meta), path("*.pdf") , emit: pdf
tuple val(meta), path("*.raw.txt") , emit: matrix
tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
path "versions.yml" , emit: versions
2020-09-10 15:45:11 +00:00
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
2020-09-10 15:45:11 +00:00
def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
"""
plotFingerprint \\
$options.args \\
2020-09-10 15:45:11 +00:00
$extend \\
--bamfiles ${bams.join(' ')} \\
--plotFile ${prefix}.plotFingerprint.pdf \\
--outRawCounts ${prefix}.plotFingerprint.raw.txt \\
--outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
--numberOfProcessors $task.cpus
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(plotFingerprint --version | sed -e "s/plotFingerprint //g")
END_VERSIONS
2020-09-10 15:45:11 +00:00
"""
}