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40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
process SEQUENZAUTILS_BAM2SEQZ {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' :
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'quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }"
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input:
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tuple val(meta), path(normalbam), path(tumourbam)
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path fasta
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path wigfile
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output:
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tuple val(meta), path("*.gz"), emit: seqz
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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 ?: "${meta.id}"
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"""
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sequenza-utils \\
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bam2seqz \\
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$args \\
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-n $normalbam \\
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-t $tumourbam \\
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--fasta $fasta \\
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-gc $wigfile \\
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-o ${prefix}.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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sequenzautils: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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