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Published November 15, 2023 | Version 3.4.0
Software Open

nf-core/sarek: Sarek 3.4.0 - Pårtetjåkko

  • 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)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/sarek/tree/3.4.0 (URL)