nf-core_modules/software/deeptools/plotheatmap/main.nf

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2020-08-05 16:17:34 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process DEEPTOOLS_PLOTHEATMAP {
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}"
"""
plotHeatmap \\
$ioptions.args \\
--matrixFile $matrix \\
--outFileName ${prefix}.plotHeatmap.pdf \\
--outFileNameMatrix ${prefix}.plotHeatmap.mat.tab
plotHeatmap --version | sed -e "s/plotHeatmap //g" > ${software}.version.txt
"""
}