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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
51 lines
1.6 KiB
Text
51 lines
1.6 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_INDEX {
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tag "$transcript_fasta"
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label "process_medium"
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publishDir "${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:'') }
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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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path genome_fasta
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path transcript_fasta
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output:
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path "salmon" , emit: index
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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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def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
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def gentrome = "gentrome.fa"
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if (genome_fasta.endsWith('.gz')) {
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get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
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gentrome = "gentrome.fa.gz"
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}
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"""
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$get_decoy_ids
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sed -i.bak -e 's/>//g' decoys.txt
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cat $transcript_fasta $genome_fasta > $gentrome
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salmon \\
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index \\
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--threads $task.cpus \\
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-t $gentrome \\
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-d decoys.txt \\
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$options.args \\
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-i salmon
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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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