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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
process MINIASM {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' :
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'quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2' }"
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input:
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tuple val(meta), path(reads), path(paf)
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output:
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tuple val(meta), path("*.gfa.gz") , emit: gfa
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tuple val(meta), path("*.fasta.gz"), emit: assembly
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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 ?: "${meta.id}"
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"""
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miniasm \\
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$args \\
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-f $reads \\
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$paf > \\
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${prefix}.gfa
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awk '/^S/{print ">"\$2"\\n"\$3}' "${prefix}.gfa" | fold > ${prefix}.fasta
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gzip -n ${prefix}.gfa
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gzip -n ${prefix}.fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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miniasm: \$( miniasm -V 2>&1 )
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END_VERSIONS
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"""
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}
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