mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +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>
52 lines
1.3 KiB
YAML
52 lines
1.3 KiB
YAML
name: ultra_pipeline
|
|
description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection
|
|
keywords:
|
|
- uLTRA
|
|
- minimap2
|
|
tools:
|
|
- ultra:
|
|
description: Splice aligner of long transcriptomic reads to genome.
|
|
homepage: https://github.com/ksahlin/uLTRA
|
|
documentation: https://github.com/ksahlin/uLTRA
|
|
tool_dev_url: https://github.com/ksahlin/uLTRA
|
|
doi: "10.1093/bioinformatics/btab540"
|
|
licence: ['GNU GPLV3']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: A fasta or fastq file of reads to align
|
|
pattern: "*.{fasta,fastq}"
|
|
- genome:
|
|
type: file
|
|
description: fasta file of reference genome
|
|
pattern: "*.fasta"
|
|
- gtf:
|
|
type: file
|
|
description: A annotation of use the genome
|
|
pattern: "*.gtf"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- sam:
|
|
type: file
|
|
description: The aligned reads in sam format
|
|
pattern: "*.sam"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@sguizard"
|
|
- "@lassefolkersen"
|
|
- "@ksahlin"
|