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d5f6985607
* add new nucmer module * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * update tests with file produced by input * Update main.nf * Update meta.yml Co-authored-by: Michael Cipriano <mcipriano@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
55 lines
2 KiB
Text
55 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process NUCMER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12"
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} else {
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container "quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12"
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}
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
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def is_compressed_query = query.getName().endsWith(".gz") ? true : false
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def fasta_name_ref = ref.getName().replace(".gz", "")
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def fasta_name_query = query.getName().replace(".gz", "")
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"""
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if [ "$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 $prefix \\
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--coords \\
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$options.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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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( 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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