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https://github.com/MillironX/nf-core_modules.git
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b5aa12ad3b
* new module: samtools/getrg * add output file to stub * add missing config * Intentionally break prettier linting * [automated] Fix linting with Prettier Co-authored-by: Phil Ewels <phil@seqera.io> Co-authored-by: nf-core-bot <core@nf-co.re>
47 lines
1.3 KiB
Text
47 lines
1.3 KiB
Text
process SAMTOOLS_GETRG {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), file("readgroups.txt"), emit: readgroup
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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samtools \\
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view \\
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-H \\
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$args \\
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$input \\
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| grep '^@RG' > readgroups.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo -e "@RG\\tID:${prefix}\\tSM:${prefix}\\tPL:ILLUMINA" > readgroups.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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