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* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
76 lines
2.9 KiB
Text
76 lines
2.9 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 MEGAHIT {
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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::megahit=1.2.9 conda-forge::pigz=2.6" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("megahit_out/*.contigs.fa.gz") , emit: contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.contigs.fa.gz") , emit: k_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.addi.fa.gz") , emit: addi_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.local.fa.gz") , emit: local_contigs
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tuple val(meta), path("megahit_out/intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs
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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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if (meta.single_end) {
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"""
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megahit \\
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-r ${reads} \\
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-t $task.cpus \\
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$options.args \\
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--out-prefix $prefix
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pigz \\
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--no-name \\
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-p $task.cpus \\
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$options.args2 \\
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megahit_out/*.fa \\
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megahit_out/intermediate_contigs/*.fa
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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END_VERSIONS
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"""
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} else {
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"""
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megahit \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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-t $task.cpus \\
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$options.args \\
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--out-prefix $prefix
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pigz \\
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--no-name \\
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-p $task.cpus \\
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$options.args2 \\
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megahit_out/*.fa \\
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megahit_out/intermediate_contigs/*.fa
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
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END_VERSIONS
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"""
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}
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}
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