mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
c25c3fe466
* 👌 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>
22 lines
902 B
Text
22 lines
902 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
|
|
include { GUNZIP } from '../../../../modules/gunzip/main.nf' addParams( options: [:] )
|
|
include { GFFREAD } from '../../../../modules/gffread/main.nf' addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )
|
|
|
|
workflow test_ultra_pipeline {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ],
|
|
file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true)
|
|
]
|
|
GUNZIP ( input )
|
|
|
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'] , checkIfExists: true)
|
|
genome = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
GFFREAD ( gtf )
|
|
|
|
ULTRA_PIPELINE ( GUNZIP.out.gunzip, genome, GFFREAD.out.gtf )
|
|
}
|