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a740a6ff48
* 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 but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
49 lines
1.6 KiB
Text
49 lines
1.6 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 CHECKM_LINEAGEWF {
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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::checkm-genome=1.1.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1"
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} else {
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container "quay.io/biocontainers/checkm-genome:1.1.3--py_1"
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}
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input:
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tuple val(meta), path(fasta)
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val fasta_ext
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output:
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tuple val(meta), path("${prefix}") , emit: checkm_output
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tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
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path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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checkm \\
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lineage_wf \\
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-t $task.cpus \\
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-f ${prefix}.tsv \\
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--tab_table \\
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--pplacer_threads $task.cpus \\
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-x $fasta_ext \\
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$options.args \\
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. \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
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END_VERSIONS
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"""
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}
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