mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
3cabc95d0e
* Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } 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 "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
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
|
|
|
|
echo \$(arriba -h | grep 'Version:' 2>&1) | sed 's/Version:\s//' > ${software}.version.txt
|
|
"""
|
|
}
|