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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
54 lines
1.8 KiB
Text
54 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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:'index', meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : 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:1.5.2--h84f40af_0"
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} else {
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container "quay.io/biocontainers/salmon:1.5.2--h84f40af_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 "versions.yml" , 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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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g")
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END_VERSIONS
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"""
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}
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