nf-core_modules/modules/salmon/quant/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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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']) }
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conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
} else {
container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
}
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input:
tuple val(meta), path(reads)
path index
path gtf
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path transcript_fasta
val alignment_mode
val lib_type
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output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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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 $reads"
}
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def strandedness_opts = [
'A', 'U', 'SF', 'SR',
'IS', 'IU' , 'ISF', 'ISR',
'OS', 'OU' , 'OSF', 'OSR',
'MS', 'MU' , 'MSF', 'MSR'
]
def strandedness = 'A'
if (lib_type) {
if (strandedness_opts.contains(lib_type)) {
strandedness = lib_type
} else {
log.info "[Salmon Quant] Invalid library type specified '--libType=${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'
}
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}
"""
salmon quant \\
--geneMap $gtf \\
--threads $task.cpus \\
--libType=$strandedness \\
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$reference \\
$input_reads \\
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$options.args \\
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-o $prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
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"""
}