nf-core_modules/software/bedtools/slop/main.nf
2021-01-29 23:17:44 -06:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BEDTOOLS_SLOP {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
input:
tuple val(meta), path(beds)
path sizes
output:
tuple val(meta), path("*.slop.bed"), emit: slopbed
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def header = params.header ? "-header":''
def pct = params.pct ? "-pct":''
def symmetry = ''
if (meta.symmetry) {
"""
slopBed -i $beds -g $sizes -b $params.b $header $pct $options.args> ${prefix}.slop.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
"""
} else {
"""
slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
"""
}
}