mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
49 lines
1.5 KiB
Text
49 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process SALMON_QUANT {
|
|
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), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
|
|
container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path index
|
|
path gtf
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}"), emit: results
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
|
|
|
|
def strandedness = meta.single_end ? 'U' : 'IU'
|
|
if (meta.strandedness == 'forward') {
|
|
strandedness = meta.single_end ? 'SF' : 'ISF'
|
|
} else if (meta.strandedness == 'reverse') {
|
|
strandedness = meta.single_end ? 'SR' : 'ISR'
|
|
}
|
|
"""
|
|
salmon quant \\
|
|
--geneMap $gtf \\
|
|
--threads $task.cpus \\
|
|
--libType=$strandedness \\
|
|
--index $index \\
|
|
$endedness \\
|
|
$options.args \\
|
|
-o $prefix
|
|
|
|
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
|
"""
|
|
}
|