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d6850f8312
* new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section Co-authored-by: suzannejin <suzanne.jin@crg.eu>
41 lines
1.4 KiB
Text
41 lines
1.4 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 SAMTOOLS_FASTQ {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::samtools=1.12" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
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} else {
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container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: fastq
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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 endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
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"""
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samtools fastq \\
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$options.args \\
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-@ $task.cpus \\
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$endedness \\
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$bam
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echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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