mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 15:38:17 -05:00
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
options = initOptions(params.options)
|
||
|
|
|
||
|
|
process DSHBIO_EXPORTSEGMENTS {
|
||
|
|
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), meta:meta, publish_by_meta:['id']) }
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(gfa)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.fa"), emit: fasta
|
||
|
|
path "*.version.txt" , emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
"""
|
||
|
|
dsh-bio \\
|
||
|
|
export-segments \\
|
||
|
|
$options.args \\
|
||
|
|
-i $gfa \\
|
||
|
|
-o ${prefix}.fa
|
||
|
|
|
||
|
|
echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|