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5a30294eec
* updated the delly/call module * Update modules/delly/call/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process DELLY_CALL {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::delly=1.1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/delly:1.1.3--h358d541_0' :
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'quay.io/biocontainers/delly:1.1.3--h358d541_0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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path exclude_bed
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path fasta
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path fai
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output:
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tuple val(meta), path("*.bcf"), emit: bcf
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tuple val(meta), path("*.csi"), emit: csi
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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 exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
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"""
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delly \\
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call \\
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${args} \\
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--outfile ${prefix}.bcf \\
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--genome ${fasta} \\
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${exclude} \\
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${input}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
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END_VERSIONS
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"""
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}
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