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38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process SEQWISH_INDUCE {
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tag "$meta.id"
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label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? 'bioconda::seqwish=0.7.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqwish:0.7.2--h2e03b76_0' :
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'quay.io/biocontainers/seqwish:0.7.2--h2e03b76_0' }"
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input:
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tuple val(meta), path(paf), path(fasta)
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output:
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tuple val(meta), path("*.gfa"), emit: gfa
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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 VERSION = '0.7.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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seqwish \\
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--threads $task.cpus \\
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--paf-alns=$paf \\
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--seqs=$fasta \\
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--gfa=${prefix}.gfa \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqwish: $VERSION
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END_VERSIONS
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"""
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}
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