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42 lines
1.1 KiB
Text
42 lines
1.1 KiB
Text
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process WHAMG {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::wham=1.8.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1':
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'quay.io/biocontainers/wham:1.8.0.1.2017.05.03--h8b12597_1' }"
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input:
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tuple val(meta), path(bam), path(bai)
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path(fasta)
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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path("*.txt") , emit: graph, optional: true
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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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whamg \\
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-x $task.cpus \\
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-f $bam \\
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-a $fasta \\
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$args \\
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> ${prefix}.vcf
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gzip ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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whamg: \$(echo \$(whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*\$//' ))
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END_VERSIONS
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"""
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}
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