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51 lines
1.4 KiB
Text
51 lines
1.4 KiB
Text
process RHOCALL_ANNOTATE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0':
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'quay.io/biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi)
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tuple val(meta), path(roh)
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path bed
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output:
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tuple val(meta), path("*_rhocall.vcf"), 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 az_bed = bed ? "-b ${bed}" : ''
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"""
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rhocall \\
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annotate \\
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$args \\
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$az_bed \\
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-r $roh \\
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-o ${prefix}_rhocall.vcf \\
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$vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_rhocall.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
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END_VERSIONS
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"""
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}
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