nf-core_modules/software/bedtools/getfasta/main.nf
2021-02-09 17:56:51 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BEDTOOLS_GETFASTA {
tag "$bed"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
path bed
path fasta
output:
path "*.fa" , emit: fasta
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${bed.baseName}${options.suffix}" : "${bed.baseName}"
"""
bedtools \\
getfasta \\
$options.args \\
-fi $fasta \\
-bed $bed \\
-fo ${prefix}.fa
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}