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40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
def VERSION = '1.0.4' // Version information not provided by tool on CLI
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process CMSEQ_POLYMUT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' :
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'quay.io/biocontainers/cmseq:1.0.4--pyhb7b1952_0' }"
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input:
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tuple val(meta), path(bam), path(bai), path(gff), path(fasta)
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output:
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tuple val(meta), path("*.txt"), emit: polymut
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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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def fasta_refid = fasta ? "-c $fasta" : ""
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def sortindex = bai ? "" : "--sortindex"
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"""
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polymut.py \\
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$args \\
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$sortindex \\
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$fasta_refid \\
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--gff_file $gff \\
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$bam > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cmseq: $VERSION
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END_VERSIONS
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"""
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}
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