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