mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
49 lines
1.7 KiB
Text
49 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ARRIBA {
|
|
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::arriba=2.1.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1"
|
|
} else {
|
|
container "quay.io/biocontainers/arriba:2.1.0--h3198e80_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
path gtf
|
|
|
|
output:
|
|
tuple val(meta), path("*.fusions.tsv") , emit: fusions
|
|
tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
|
|
"""
|
|
arriba \\
|
|
-x $bam \\
|
|
-a $fasta \\
|
|
-g $gtf \\
|
|
-o ${prefix}.fusions.tsv \\
|
|
-O ${prefix}.fusions.discarded.tsv \\
|
|
$blacklist \\
|
|
$options.args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|