Published October 14, 2025
| Version 3.6.0
Software
Open
nf-core/sarek: Sarek 3.6.0 - Kvikkjokk
Creators
- Maxime U Garcia
- Friederike Hanssen1
- Anders Sune Pedersen2
- Gisela Gabernet
- WackerO
- SusiJo
- Adam Talbot3
- nf-core bot
- Chela James4
- Simon Pearce
- Alexander Peltzer5
- nickhsmith
- José Fernández Navarro
- Famke Bäuerle6
- Edmund Miller3
- JĂşlia Mir Pedrol
- Francesco Lescai7
- Grant Neilson8
- Francisco MartĂnez9
- kjellinjonas
- Bekir ErgĂĽner10
- Matthias De Smet11
- Pierre Lindenbaum12
- Nicolás A. Schcolnicov13
- David Mas-Ponte14
- Malin Larsson15
- Abhinav Sharma16
- Robert Syme17
- Nicolas Vannieuwkerke18
- Chase Mateusiak19
- 1. Seqera
- 2. Dep. of Molecular Medicine (MOMA)
- 3. @seqeralabs
- 4. Fondazione Human Technopole
- 5. Boehringer Ingelheim
- 6. University of Tuebingen
- 7. University of Pavia
- 8. CoSyne Therapeutics
- 9. INCLIVA
- 10. Exscientia
- 11. @CenterForMedicalGeneticsGhent
- 12. INSERM
- 13. ZS Associates
- 14. UW
- 15. SciLifeLab
- 16. @biosharp-dotnet
- 17. Seqera Labs
- 18. Center for Medical Genetics Ghent
- 19. Washington University
Description
What's Changed
Main new features
🧬 Lots of improvements around UMI support (#1937, @SPPearce) ⏩ Parabricks support (#1804, @famosab) 🔍 Muse (#1744, @famosab) and Sentieon TNScope (#1934, @SPPearce) 📜 MSISensor2 (#1965, @maxulysse) 🦖 Varlociraptor (#1940, @famosab) ◀️ Normalization of variants (#1770, @Patricie34 & @maxulysse) 🖖 bbsplit (#1983, @apsteinberg, @tobsecret & @FriederikeHanssen)
Changed
- Version updates:
- VEP cache updated to v115.2
- SnpEff updated to v5.3.0a (SnpEff cache downgraded to 99 since 105 is not available at the moment)
- GATK4 to 4.6.1.0
- DeepVariant to 1.9.0
- Freebayes to 1.3.10 with QUAL filtering
- Workflow improvements:
- Enhanced metro map
- Doubled default process time
- Improved sample validation
- Complete test migration:
- All pytest tests migrated to nf-test framework for better testing infrastructure
Fixed
- Input validation: Better samplesheet validation in #1842 by @nvnieuwk and #1858 by @kjellinjonas and bugfix addReadgroupToMeta in #1849 by @thiago-miller
- CNVkit compatibility: Fixed
--no_intervalsusage and CPU allocation in #1928 by @SPPearce - DeepVariant configuration: Added
--sample_nameargument when meta.sample available in #1992 by @matthdsm
New Parameters
--freebayes_filter--msisensor2_models--sentieon_consensus--umi_base_skip--umi_in_read_header--umi_length--umi_location--umi_tag--varlociraptor_chunk_size--varlociraptor_scenario_germline--varlociraptor_scenario_somatic--varlociraptor_scenario_tumor_only
Full Changelog:Â 3.5.1...3.6.0
Files
nf-core/sarek-3.6.0.zip
Files
(15.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:61f59280e3341c855c0328b8ce69dc2e
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15.4 MB | Preview Download |
Additional details
Related works
- Is supplement to
- Software: https://github.com/nf-core/sarek/tree/3.6.0 (URL)
Software
- Repository URL
- https://github.com/nf-core/sarek