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527ccdb419
* add racon * add miniasm module * edit miniasm module * edit miniasm module * Update tests/modules/racon/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update tests/modules/racon/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/miniasm/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update main.nf Add some spaces. * Update meta.yml Correct DOI * Update main.nf * Apply suggestions from code review * Update tests/modules/miniasm/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.5 KiB
Text
48 lines
1.5 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 MINIASM {
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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::miniasm=0.3_r179" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2"
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} else {
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container "quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2"
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}
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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miniasm \\
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$options.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 ${prefix}.fasta
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( miniasm -V 2>&1 )
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END_VERSIONS
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"""
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}
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