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* 👌 IMPROVE: Update .gitignore * 📦 Add ultra module * 👌 IMPROVE: Update test input * 👌 IMPROVE: Update and clean code - Update to last versions.yml file - Update meta.yml - Correct typos * 👌 IMPROVE: Update output channels + Rename following subtool * 👌 IMPROVE: Remove old ultre files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 👌 IMPROVE: Remove old ultra files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 🐛 Fix: add unsaved modifications * 🐛 FIX: Remove one inconstant md5sum * 🐛 FIX: Grab software name using ${getSoftwareName(task.process)} * 🐛 FIX: Remove md5sums for pickle files (not constant). * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 👌 IMPROVE: update output directory, update meta.yml * 👌 IMPROVE: Use modules to gunzip and sort gtf * 🐛 FIX: Set up channel correctly * 👌 IMPROVE: Remove pickles files and databases Those data might be useful in a debugging purpose. * Apply suggestions from code review * Update main.nf * 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd) * 👌 IMPROVE: Sort tags in test.yml * align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ULTRA_PIPELINE {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
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} else {
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container "quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
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}
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input:
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tuple val(meta), path(reads)
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path genome
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path gtf
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output:
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tuple val(meta), path("*.sam"), emit: sam
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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uLTRA \\
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pipeline \\
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--t $task.cpus \\
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--prefix $prefix \\
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$options.args \\
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$genome \\
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$gtf \\
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$reads \\
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./
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( uLTRA --version|sed 's/uLTRA //g' )
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END_VERSIONS
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"""
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}
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