nf-core_modules/modules/salmon/quant/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

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// 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
"""
}