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48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
process NUCMER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' :
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'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }"
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input:
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tuple val(meta), path(ref), path(query)
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output:
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tuple val(meta), path("*.delta") , emit: delta
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tuple val(meta), path("*.coords"), emit: coords
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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 ?: "${meta.id}"
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def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
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def is_compressed_query = query.getName().endsWith(".gz") ? true : false
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def fasta_name_ref = ref.getName().replace(".gz", "")
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def fasta_name_query = query.getName().replace(".gz", "")
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"""
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if [ "$is_compressed_ref" == "true" ]; then
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gzip -c -d $ref > $fasta_name_ref
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fi
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if [ "$is_compressed_query" == "true" ]; then
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gzip -c -d $query > $fasta_name_query
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fi
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nucmer \\
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-p $prefix \\
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--coords \\
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$args \\
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$fasta_name_ref \\
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$fasta_name_query
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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nucmer: \$( nucmer --version 2>&1 | grep "version" | sed -e "s/NUCmer (NUCleotide MUMmer) version //g; s/nucmer//g;" )
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END_VERSIONS
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"""
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}
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