mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
52 lines
1.7 KiB
Text
52 lines
1.7 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
process STRINGTIE {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
|
|
//container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
|
|
|
|
conda (params.conda ? "bioconda::stringtie=2.1.4" : null)
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path gtf
|
|
val options
|
|
|
|
output:
|
|
tuple val(meta), path("*.coverage.gtf") , emit: coverage_gtf
|
|
tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
|
|
tuple val(meta), path("*.txt") , emit: abundance
|
|
tuple val(meta), path("*.ballgown") , emit: ballgown
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def ioptions = initOptions(options)
|
|
def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
|
|
|
|
def strandedness = ''
|
|
if (meta.strandedness == 'forward') {
|
|
strandedness = '--fr'
|
|
} else if (meta.strandedness == 'reverse') {
|
|
strandedness = '--rf'
|
|
}
|
|
"""
|
|
stringtie \\
|
|
$bam \\
|
|
$strandedness \\
|
|
-G $gtf \\
|
|
-o ${prefix}.transcripts.gtf \\
|
|
-A ${prefix}.gene_abundance.txt \\
|
|
-C ${prefix}.coverage.gtf \\
|
|
-b ${prefix}.ballgown \\
|
|
$ioptions.args
|
|
|
|
stringtie --version > ${software}.version.txt
|
|
"""
|
|
}
|