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e937c7950a
* 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
44 lines
1.5 KiB
Text
44 lines
1.5 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 BISMARK_ALIGN {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
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} else {
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container "quay.io/biocontainers/bismark:0.23.0--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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output:
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tuple val(meta), path("*bam") , emit: bam
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tuple val(meta), path("*report.txt"), emit: report
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tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped
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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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
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"""
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bismark \\
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$fastq \\
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$options.args \\
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--genome $index \\
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--bam
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echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
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"""
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}
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