2020-09-10 15:45:11 +00:00
|
|
|
// Import generic module functions
|
|
|
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
|
|
|
|
|
|
process DEEPTOOLS_PLOTPROFILE {
|
|
|
|
|
tag "$meta.id"
|
|
|
|
|
label 'process_low'
|
|
|
|
|
publishDir "${params.outdir}",
|
|
|
|
|
mode: params.publish_dir_mode,
|
|
|
|
|
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
|
|
|
|
|
|
container "quay.io/biocontainers/deeptools:3.4.3--py_0"
|
|
|
|
|
//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
|
|
|
|
|
|
|
|
|
|
conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
|
|
|
|
|
|
|
|
|
|
input:
|
|
|
|
|
tuple val(meta), path(matrix)
|
|
|
|
|
val options
|
|
|
|
|
|
|
|
|
|
output:
|
|
|
|
|
tuple val(meta), path("*.pdf"), emit: pdf
|
|
|
|
|
tuple val(meta), path("*.tab"), emit: table
|
|
|
|
|
path "*.version.txt" , emit: version
|
|
|
|
|
|
|
|
|
|
script:
|
|
|
|
|
def software = getSoftwareName(task.process)
|
|
|
|
|
def ioptions = initOptions(options)
|
|
|
|
|
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
|
|
|
|
"""
|
|
|
|
|
plotProfile \\
|
|
|
|
|
$ioptions.args \\
|
|
|
|
|
--matrixFile $matrix \\
|
|
|
|
|
--outFileName ${prefix}.plotProfile.pdf \\
|
|
|
|
|
--outFileNameData ${prefix}.plotProfile.tab
|
|
|
|
|
|
|
|
|
|
plotProfile --version | sed -e "s/plotProfile //g" > ${software}.version.txt
|
|
|
|
|
"""
|
|
|
|
|
}
|
