nf-core_modules/software/bedtools/slop/main.nf

44 lines
1.3 KiB
Text
Raw Normal View History

// 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) }
2021-02-07 21:32:20 +00:00
conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
2021-01-28 14:24:33 +00:00
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
2021-01-28 12:24:03 +00:00
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
2021-01-08 19:44:02 +00:00
input:
2021-02-07 21:32:20 +00:00
tuple val(meta), path(bed)
path sizes
output:
2021-02-07 21:32:20 +00:00
tuple val(meta), path("*.bed"), emit: bed
path "*.version.txt" , emit: version
script:
2021-01-28 12:24:03 +00:00
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools \\
slop \\
2021-02-07 21:32:20 +00:00
-i $bed \\
2021-01-28 12:24:03 +00:00
-g $sizes \\
$options.args \\
2021-02-07 21:32:20 +00:00
> ${prefix}.bed
2021-01-28 12:24:03 +00:00
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}