nf-core_modules/software/deeptools/plotfingerprint/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

46 lines
1.8 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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']) }
conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
} else {
container "quay.io/biocontainers/deeptools:3.5.0--py_0"
}
input:
tuple val(meta), path(bams), path(bais)
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 "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
"""
plotFingerprint \\
$options.args \\
$extend \\
--bamfiles ${bams.join(' ')} \\
--plotFile ${prefix}.plotFingerprint.pdf \\
--outRawCounts ${prefix}.plotFingerprint.raw.txt \\
--outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\
--numberOfProcessors $task.cpus
plotFingerprint --version | sed -e "s/plotFingerprint //g" > ${software}.version.txt
"""
}