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39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
process GSTAMA_MERGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' :
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'quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0' }"
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input:
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tuple val(meta), path(bed)
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path filelist
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output:
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tuple val(meta), path("*.bed") , emit: bed
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tuple val(meta), path("*_gene_report.txt") , emit: gene_report
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tuple val(meta), path("*_merge.txt") , emit: merge
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tuple val(meta), path("*_trans_report.txt"), emit: trans_report
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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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tama_merge.py \\
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-f $filelist \\
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-d merge_dup \\
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-p ${prefix} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gstama: \$( tama_merge.py -version | head -n1 )
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END_VERSIONS
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"""
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}
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