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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 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
25 lines
963 B
Text
25 lines
963 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
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include { GUNZIP } from '../../../../modules/gunzip/main.nf' addParams( options: [:] )
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include { GFFREAD } from '../../../../modules/gffread/main.nf' addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )
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workflow test_ultra_pipeline {
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fastq = file(params.test_data['homo_sapiens']['pacbio']['hifi'] , checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'] , checkIfExists: true)
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genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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GUNZIP ( fastq )
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GFFREAD ( gtf )
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GUNZIP
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.out
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.gunzip
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.map { [ [ id:'test', single_end:false ], it ] }
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.set { input }
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ULTRA_PIPELINE ( input, genome, GFFREAD.out.gtf )
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}
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