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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
71 lines
2.7 KiB
Text
71 lines
2.7 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 HIFIASM {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::hifiasm=0.15.4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0"
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} else {
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container "quay.io/biocontainers/hifiasm:0.15.4--h2e03b76_0"
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}
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input:
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tuple val(meta), path(reads)
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path paternal_kmer_dump
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path maternal_kmer_dump
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val use_parental_kmers
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output:
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tuple val(meta), path("*.r_utg.gfa") , emit: raw_unitigs
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tuple val(meta), path("*.ec.bin") , emit: corrected_reads
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tuple val(meta), path("*.ovlp.source.bin") , emit: source_overlaps
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tuple val(meta), path("*.ovlp.reverse.bin"), emit: reverse_overlaps
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tuple val(meta), path("*.p_utg.gfa") , emit: processed_unitigs, optional: true
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tuple val(meta), path("*.asm.p_ctg.gfa") , emit: primary_contigs , optional: true
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tuple val(meta), path("*.asm.a_ctg.gfa") , emit: alternate_contigs, optional: true
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tuple val(meta), path("*.hap1.p_ctg.gfa") , emit: paternal_contigs , optional: true
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tuple val(meta), path("*.hap2.p_ctg.gfa") , emit: maternal_contigs , optional: true
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (use_parental_kmers) {
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"""
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hifiasm \\
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$options.args \\
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-o ${prefix}.asm \\
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-t $task.cpus \\
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-1 $paternal_kmer_dump \\
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-2 $maternal_kmer_dump \\
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$reads
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1)
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END_VERSIONS
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"""
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} else { // Phasing with Hi-C data is not supported yet
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"""
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hifiasm \\
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$options.args \\
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-o ${prefix}.asm \\
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-t $task.cpus \\
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$reads
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1)
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END_VERSIONS
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"""
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}
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}
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