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40 lines
1 KiB
Text
40 lines
1 KiB
Text
process MEDAKA {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' :
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'quay.io/biocontainers/medaka:1.4.4--py38h130def0_0' }"
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input:
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tuple val(meta), path(reads), path(assembly)
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output:
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tuple val(meta), path("*.fa.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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medaka_consensus \\
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-t $task.cpus \\
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$args \\
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-i $reads \\
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-d $assembly \\
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-o ./
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mv consensus.fasta ${prefix}.fa
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gzip -n ${prefix}.fa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' )
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END_VERSIONS
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"""
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}
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