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bd2baa1e7c
* 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 * Added, just need to finish tests once we have bacterial data * Add prelim test data * Fix version reporting * Add tests based on proposed test-dataset * Finalise new testdata * Fix md5sum issue by removing it... * Update main.nf * 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>
53 lines
2 KiB
Text
53 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 MAXBIN2 {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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::maxbin2=2.2.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2"
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} else {
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container "quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2"
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}
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input:
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tuple val(meta), path(contigs), path(reads), path(abund)
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output:
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tuple val(meta), path("*.fasta.gz") , emit: binned_fastas
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tuple val(meta), path("*.summary") , emit: summary
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tuple val(meta), path("*.log.gz") , emit: log
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tuple val(meta), path("*.marker.gz") , emit: marker_counts
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tuple val(meta), path("*.noclass.gz") , emit: unbinned_fasta
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tuple val(meta), path("*.tooshort.gz"), emit: tooshort_fasta
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tuple val(meta), path("*_bin.tar.gz") , emit: marker_bins , optional: true
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tuple val(meta), path("*_gene.tar.gz"), emit: marker_genes, optional: true
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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 associate_files = reads ? "-reads $reads" : "-abund $abund"
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"""
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run_MaxBin.pl \\
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-contig $contigs \\
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$associate_files \\
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-thread $task.cpus \\
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$options.args \\
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-out $prefix
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gzip *.fasta *.noclass *.tooshort *log *.marker
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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maxbin2: \$( run_MaxBin.pl -v | head -n 1 | sed 's/MaxBin //' )
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END_VERSIONS
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"""
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}
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