mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
e621f78757
* Update salmon/quant to provide '--libType A' option * Modify lib_type description to be a string * Update tests * lyb_type can be explicitly overwrite * Update main.nf * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
77 lines
2.5 KiB
Text
77 lines
2.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
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), meta:meta, publish_by_meta:['id']) }
|
|
|
|
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
|
|
} else {
|
|
container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path index
|
|
path gtf
|
|
path transcript_fasta
|
|
val alignment_mode
|
|
val lib_type
|
|
|
|
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 reference = "--index $index"
|
|
def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
|
|
if (alignment_mode) {
|
|
reference = "-t $transcript_fasta"
|
|
input_reads = "-a $reads"
|
|
}
|
|
|
|
def strandedness_opts = [
|
|
'A', 'U', 'SF', 'SR',
|
|
'IS', 'IU' , 'ISF', 'ISR',
|
|
'OS', 'OU' , 'OSF', 'OSR',
|
|
'MS', 'MU' , 'MSF', 'MSR'
|
|
]
|
|
def strandedness = 'A'
|
|
if (lib_type) {
|
|
if (strandedness_opts.contains(lib_type)) {
|
|
strandedness = lib_type
|
|
} else {
|
|
log.info "[Salmon Quant] Invalid library type specified '--libType=${lib_type}', defaulting to auto-detection with '--libType=A'."
|
|
}
|
|
} else {
|
|
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 \\
|
|
$reference \\
|
|
$input_reads \\
|
|
$options.args \\
|
|
-o $prefix
|
|
|
|
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
|
"""
|
|
}
|