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080320765c
* 📦 NEW: Add bamtools/convert module * 👌 IMPROVE: Update output channel name, Add tests for each output format * 👌 IMPROVE: Add error test * 🐛 FIX: Remove custom tags Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process BAMTOOLS_CONVERT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
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'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
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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("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
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if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
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m = args =~ /-format ([a-z]+)/
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ext = m[0][1]
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"""
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bamtools \\
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convert \\
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$args \\
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-in $bam \\
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-out ${prefix}.${ext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
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END_VERSIONS
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"""
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}
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