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a6cb75174b
* Add optional variant catalog input * fix for no variant catalog test Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com> Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
36 lines
1 KiB
Text
36 lines
1 KiB
Text
process STRANGER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
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'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(vcf)
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path variant_catalog
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output:
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tuple val(meta), path("*.gz"), emit: vcf
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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 options_variant_catalog = variant_catalog ? "--repeats-file $variant_catalog" : ""
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"""
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stranger \\
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$args \\
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$vcf \\
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$options_variant_catalog | gzip --no-name > ${prefix}.vcf.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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stranger: \$( stranger --version )
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END_VERSIONS
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"""
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}
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