nf-core_modules/software/homer/annotatepeaks/main.nf

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2020-08-05 16:16:56 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
def VERSION = '4.11'
process HOMER_ANNOTATEPEAKS {
tag "$meta.id"
label 'process_medium'
publishDir "${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/homer:4.11--pl526h9a982cc_2"
//container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
conda (params.conda ? "bioconda::homer=4.11" : null)
input:
tuple val(meta), path(peak)
path fasta
path gtf
val options
output:
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
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}"
"""
annotatePeaks.pl \\
$peak \\
$fasta \\
$ioptions.args \\
-gtf $gtf \\
-cpu $task.cpus \\
> ${prefix}.annotatePeaks.txt
echo $VERSION > ${software}.version.txt
"""
}