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35 lines
1.3 KiB
Text
35 lines
1.3 KiB
Text
process MANTA_CONVERTINVERSION {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::manta=1.6.0 bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0':
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'quay.io/biocontainers/mulled-v2-40295ae41112676b05b649e513fe7000675e9b84:0b4be2c719f99f44df34be7b447b287bb7f86e01-0' }"
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input:
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tuple val(meta), path(vcf)
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path fasta
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output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
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tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
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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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convertInversion.py \$(which samtools) $fasta $vcf | bgzip --threads $task.cpus > ${prefix}.vcf.gz
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tabix ${prefix}.vcf.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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manta: \$( configManta.py --version )
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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