Published November 15, 2023
| Version 3.4.0
Software
Open
nf-core/sarek: Sarek 3.4.0 - Pårtetjåkko
Creators
- Maxime U Garcia1
- Friederike Hanssen2
- Anders Sune Pedersen3
- Gisela Gabernet
- WackerO
- SusiJo
- Adam Talbot4
- Chela James5
- Bekir Ergüner6
- Alexander Peltzer7
- nickhsmith
- José Fernández Navarro
- nf-core bot
- Júlia Mir Pedrol
- Grant Neilson8
- Edmund Miller9
- Simon Pearce
- David Mas-Ponte10
- Malin Larsson11
- Abhinav Sharma12
- Adrian Lärkeryd13
- Francesco Lescai
- Lasse Folkersen14
- Lucia Conde15
- Robert Syme16
- Raquel Manzano17
- Matilda Åslin18
- BarryDigby
- Harshil Patel16
- Paul Cantalupo
- 1. @seqeralabs | Stockholm
- 2. QBiC
- 3. Dep. of Molecular Medicine (MOMA)
- 4. @seqeralabs
- 5. Fondazione Human Technopole
- 6. Exscientia
- 7. Boehringer Ingelheim
- 8. WeWork
- 9. @Functional-Genomics-Lab
- 10. UW
- 11. SciLifeLab
- 12. @biosharp-dotnet
- 13. ICR
- 14. NucleusGenomics | mynucleus.com
- 15. University College London
- 16. Seqera Labs
- 17. Cancer Research UK
- 18. Uppsala University, SciLifeLab Genomics, NGI Uppsala
Description
What's Changed
New tools:
- Dnascope was added by @asp8200 in https://github.com/nf-core/sarek/pull/1193, https://github.com/nf-core/sarek/pull/1280
- Add NGSCheckMate by @SPPearce in https://github.com/nf-core/sarek/pull/1252
- Add CnvkKt Genemetrics by @grantn5 in https://github.com/nf-core/sarek/pull/1223
- Add Bcftools annotate by @grantn5 in https://github.com/nf-core/sarek/pull/1267
Refactoring
- Add an nf-test CI by @adamrtalbot in https://github.com/nf-core/sarek/pull/1288, https://github.com/nf-core/sarek/pull/1289, https://github.com/nf-core/sarek/pull/1290
- Created subworkflow for parsing samplesheet with nf-test by @RaqManzano in https://github.com/nf-core/sarek/pull/1286
- Update config files and other minor code polishing by @maxulysse in https://github.com/nf-core/sarek/pull/1325
Bug fixes and other updates
- Fix bug with params.json file writing on s3 by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1318
- Fix links to docs by @maxulysse in https://github.com/nf-core/sarek/pull/1328
- Fix nf-prov usage by @maxulysse in https://github.com/nf-core/sarek/pull/1301
- Fix remove use_annotation_cache_keys params by @maxulysse in https://github.com/nf-core/sarek/pull/1298
- Fix clashes of config of FILTERVARIANTTRANCHES in different subworkflows by @asp8200 in https://github.com/nf-core/sarek/pull/1315
- Fix several bugs for joint calling with Mutect2 by @FriederikeHanssen & @maxulysse in https://github.com/nf-core/sarek/pull/1277, https://github.com/nf-core/sarek/pull/1309
- Update modules by @maxulysse & @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1304, https://github.com/nf-core/sarek/pull/1311, https://github.com/nf-core/sarek/pull/1327
- Add SnpEff to full sized tests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1330
- Proper usage of vep_version by @maxulysse in https://github.com/nf-core/sarek/pull/1303
- Update docs by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1278, https://github.com/nf-core/sarek/pull/1317
- Adding labels to the local modules by @asp8200 in https://github.com/nf-core/sarek/pull/1287
New Contributors
- @grantn5 made their first contribution in https://github.com/nf-core/sarek/pull/1223
- @RaqManzano made their first contribution in https://github.com/nf-core/sarek/pull/1286
- @SPPearce made their first contribution in https://github.com/nf-core/sarek/pull/1252
Full Changelog: https://github.com/nf-core/sarek/compare/3.3.2...3.4.0
Files
nf-core/sarek-3.4.0.zip
Files
(15.2 MB)
Name | Size | Download all |
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md5:566398c3481d90d99e736c9992e7f001
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Additional details
Related works
- Is supplement to
- Software: https://github.com/nf-core/sarek/tree/3.4.0 (URL)