nf-core

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Published August 7, 2024 | Version 3.4.3
Software Open

nf-core/sarek: Sarek 3.4.3 - Loametjåhkkå

Creators

  • 1. @seqeralabs
  • 2. Seqera
  • 3. Dep. of Molecular Medicine (MOMA)
  • 4. Fondazione Human Technopole
  • 5. Boehringer Ingelheim
  • 6. University of Pavia
  • 7. Cosyne Therapeutics
  • 8. INCLIVA
  • 9. Exscientia
  • 10. INSERM
  • 11. ZS Associates
  • 12. UW
  • 13. SciLifeLab
  • 14. @biosharp-dotnet
  • 15. Seqera Labs
  • 16. Washington University
  • 17. University of Tuebingen
  • 18. University College London
  • 19. NucleusGenomics | mynucleus.com
  • 20. ICR

Description

What's Changed

Added

  • Add support for fastq.gz.spring-files as input by @asp8200 in https://github.com/nf-core/sarek/pull/1534, https://github.com/nf-core/sarek/pull/1573
  • Add a specific cnvkit/call module to perform calling from cns files by @lescai in https://github.com/nf-core/sarek/pull/1502
  • Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in https://github.com/nf-core/sarek/pull/1502

Changed

  • Template update for nf-core/tools v2.14.1
  • Unify handling of params.cnvkit_reference uniform across the three subworkflows (germline, tumour only, tumour-normal) by @lescai in https://github.com/nf-core/sarek/pull/1502
  • Simplify logic in args management by @maxulysse in https://github.com/nf-core/sarek/pull/1521
  • Update vep cache version to 111 by @maxulysse in https://github.com/nf-core/sarek/pull/1557
  • Cleanup + update modules by @maxulysse in https://github.com/nf-core/sarek/pull/1545
  • Updating documentation by @asp8200 in https://github.com/nf-core/sarek/pull/1556 and by @maxulysse in https://github.com/nf-core/sarek/pull/1570

Fixed

  • FIX: mapped bam and bai published in the same folder by @asp8200 in https://github.com/nf-core/sarek/pull/1541
  • FIX: typo (strelka2 -> strelka) by @maxulysse in https://github.com/nf-core/sarek/pull/1536
  • FIX: Typo build_from_index -> build_only_index by @maxulysse in https://github.com/nf-core/sarek/pull/1547
  • FIX: Correct vep_cache_path_full when refseq/merged option is present by @YeHW in https://github.com/nf-core/sarek/pull/1563
  • Remove snapshot from Haplotypecaller tests by @maxulysse in https://github.com/nf-core/sarek/pull/1596
  • Remove snapshot from Deepvariant tests by @maxulysse in https://github.com/nf-core/sarek/pull/1597
  • Remove empty outdirs by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1612
  • Remove legacy configs of CUSTOM_DUMPSOFTWAREVERSIONS by @asp8200 in https://github.com/nf-core/sarek/pull/1542

New Contributors

  • @famosab made their first contribution in https://github.com/nf-core/sarek/pull/1527
  • @YeHW made their first contribution in https://github.com/nf-core/sarek/pull/1563

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.2...3.4.3

Files

nf-core/sarek-3.4.3.zip

Files (13.3 MB)

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md5:5d5587c1c52916aacd41038a290ff856
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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/sarek/tree/3.4.3 (URL)

Software

Repository URL
https://github.com/nf-core/sarek