Published September 13, 2023
| Version 3.3.0
Software
Open
nf-core/sarek: Sarek 3.3.0 - Rapaselet
Creators
- Maxime U Garcia1
- Friederike Hanssen2
- Anders Sune Pedersen3
- Gisela Gabernet
- WackerO
- SusiJo
- Chela James4
- Adam Talbot5
- Bekir Ergüner6
- Alexander Peltzer7
- nickhsmith
- José Fernández Navarro
- nf-core bot
- Júlia Mir Pedrol
- Edmund Miller
- David Mas-Ponte8
- Malin Larsson9
- Szilveszter Juhos10
- ameynert
- Abhinav Sharma11
- Adrian Lärkeryd12
- Francesco Lescai
- Lasse Folkersen13
- Lucia Conde14
- Robert Syme15
- Matilda Åslin16
- BarryDigby
- Harshil Patel15
- Paul Cantalupo
- Phil Ewels5
- 1. @seqeralabs | Stockholm
- 2. QBiC
- 3. Dep. of Molecular Medicine (MOMA)
- 4. Fondazione Human Technopole
- 5. @seqeralabs
- 6. Exscientia
- 7. Boehringer Ingelheim
- 8. UW
- 9. SciLifeLab
- 10. Morgan Stanley Budapest
- 11. @biosharp-dotnet
- 12. ICR
- 13. NucleusGenomics | mynucleus.com
- 14. University College London
- 15. Seqera Labs
- 16. Uppsala University, SciLifeLab Genomics, NGI Uppsala
Description
What's Changed
- FEAT: Mutect2 multi sample subworkflow by @berguner in https://github.com/nf-core/sarek/pull/1013
- FEAT: Sentieon DNAseq workflow by @asp8200 in https://github.com/nf-core/sarek/pull/994. https://github.com/nf-core/sarek/pull/1002. https://github.com/nf-core/sarek/pull/1007. https://github.com/nf-core/sarek/pull/1123. https://github.com/nf-core/sarek/pull/1044.
- FEAT: Greatly improve tower.yml file by @maxulysse in https://github.com/nf-core/sarek/pull/1197
- FEAT: Use annotation-cache and update VEP to v110 by @maxulysse in https://github.com/nf-core/sarek/pull/1122
- FEAT: Added
nf-validationfor samplesheet validation by @mirpedrol in https://github.com/nf-core/sarek/pull/1059 - Update of nf-core modules. https://github.com/nf-core/sarek/pull/1180. https://github.com/nf-core/sarek/pull/1160. https://github.com/nf-core/sarek/pull/1174. https://github.com/nf-core/sarek/pull/1227. https://github.com/nf-core/sarek/pull/1224
- Improved docs. https://github.com/nf-core/sarek/pull/1163. https://github.com/nf-core/sarek/pull/1138 (@rhagenson), https://github.com/nf-core/sarek/pull/1192 (@JohannesKersting). https://github.com/nf-core/sarek/pull/1222 (@adamrtalbot). https://github.com/nf-core/sarek/pull/1166. https://github.com/nf-core/sarek/pull/1179 (@robsyme). https://github.com/nf-core/sarek/pull/1183.
snpeff_dbparameter validation by @maxulysse in https://github.com/nf-core/sarek/pull/1143- FIX: Exome flag for Manta by @maxulysse in https://github.com/nf-core/sarek/pull/1149
- FIX: Move all vep args from ext.args to params.vep_custom_args by @maxulysse in https://github.com/nf-core/sarek/pull/1157
- FIX: GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1173
- FIX: Improved workflows for GHA by @adamrtalbot in https://github.com/nf-core/sarek/pull/1200
- FIX: Remove Nextflow caching for CI-tests by @Emiller88 in https://github.com/nf-core/sarek/pull/1202
- FIX: Remove singularity tests from GHA by @maxulysse in https://github.com/nf-core/sarek/pull/1218
- FIX: Better coverage for all tests by @maxulysse in https://github.com/nf-core/sarek/pull/1225, https://github.com/nf-core/sarek/pull/1216
- FIX: GVCF-files are published also when all intervals are processed at once by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1172
- FIX: Don't pass in intervals file to control-freec for WGS by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1214
- FIX: getpileupsummary should not run if no germline resource is provided by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1171
- @nicorap made their first contribution in https://github.com/nf-core/sarek/pull/1111
- @rhagenson made their first contribution in https://github.com/nf-core/sarek/pull/1138
- @berguner made their first contribution in https://github.com/nf-core/sarek/pull/1013
- @mirpedrol made their first contribution in https://github.com/nf-core/sarek/pull/1059
- @ATpoint made their first contribution in https://github.com/nf-core/sarek/pull/1166
- @JohannesKersting made their first contribution in https://github.com/nf-core/sarek/pull/1192
Full Changelog: https://github.com/nf-core/sarek/compare/3.2.3...3.3.0
Files
nf-core/sarek-3.3.0.zip
Files
(15.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/nf-core/sarek/tree/3.3.0 (URL)