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Published December 17, 2021 | Version 3.5
Software Open

nf-core/rnaseq: nf-core/rnaseq v3.5 - Copper Chameleon

Authors/Creators

  • 1. Seqera Labs
  • 2. Science for Life Laboratory
  • 3. Boehringer Ingelheim
  • 4. @czbiohub
  • 5. Medical University of Innsbruck
  • 6. Inivata
  • 7. CZ BioHub
  • 8. @qbicsoftware
  • 9. Harvard Chan School of Public Health
  • 10. Francis Crick Institute @crickbabs
  • 11. QBiC
  • 12. @SciLifeLab | Karolinska Institutet
  • 13. The Francis Crick Institute
  • 14. @maizeumn
  • 15. TU Munich
  • 16. QBiC @qbicsoftware
  • 17. University College London
  • 18. @ScilifelabDataCentre

Description

[3.5] - 2021-12-17 Enhancements & fixes
  • Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
    • Removed --publish_dir_mode as it is no longer required for the new syntax
  • Bump minimum Nextflow version from 21.04.0 -> 21.10.3
  • Updated pipeline template to nf-core/tools 2.2
  • [#664] - Conflict of library names for technical replicates
  • [#720] - KeyError 'gene_id' in salmon_tx2gene.py
  • [#724] - Deal with warnings generated when native NF processes are used
  • [#725] - Untar needs --no-same-owner on DNAnexus
  • [#727] - Fix transcriptome staging issues on DNAnexus for rsem/prepareference
  • [#728] - Add RSeQC TIN.py as a quality metric for the pipeline

Files

nf-core/rnaseq-3.5.zip

Files (5.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/nf-core/rnaseq/tree/3.5 (URL)