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https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
61 lines
1.9 KiB
Text
61 lines
1.9 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SALMON_QUANT {
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tag "$meta.id"
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label "process_medium"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
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} else {
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container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
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}
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input:
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tuple val(meta), path(reads)
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path index
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path gtf
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path transcript_fasta
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val alignment_mode
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = "--index $index"
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def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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if (alignment_mode) {
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reference = "-t $transcript_fasta"
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input_reads = "-a $reads"
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}
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def strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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strandedness = meta.single_end ? 'SF' : 'ISF'
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} else if (meta.strandedness == 'reverse') {
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strandedness = meta.single_end ? 'SR' : 'ISR'
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}
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"""
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salmon quant \\
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--geneMap $gtf \\
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--threads $task.cpus \\
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--libType=$strandedness \\
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$reference \\
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$input_reads \\
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$options.args \\
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-o $prefix
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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"""
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}
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