nf-core

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Published April 3, 2024 | Version 2.9.0
Software Open

nf-core/ampliseq: Ampliseq Version 2.9.0

Authors/Creators

  • 1. QBiC
  • 2. National Bioinformatics Infrastructure Sweden (NBIS)
  • 3. Boehringer Ingelheim
  • 4. Linnaeus University & Stockholm University
  • 5. MemVerge
  • 6. Minderoo Foundation
  • 7. @NBISweden
  • 8. HUJI
  • 9. QBiC @qbicsoftware
  • 10. Lund University
  • 11. @seqeralabs
  • 12. @FredHutch
  • 13. STFC Hartree Centre
  • 14. Seqera
  • 15. CNRS, Station Biologique
  • 16. Robert Bosch GmbH

Description

nf-core/ampliseq version 2.9.0 - 2024-04-03

Summary of changes

  • added multiple regions analysis (including 5R / SMURF / q2-sidle), integrating pipesidle and its software container with 1 & 2.
  • template update 2.11 to 2.13.1
  • several bug fixes

Detailed changes

Added

  • #700 - Optional --save_intermediates to publish QIIME2 data objects (.qza) and visualisation objects (.qzv)
  • #702,#723,#728,#729 - Add multiple regions analysis (including 5R / SMURF / q2-sidle)

Changed

  • #719 - Versions of all (instead of selected) processes are now exported to pipeline_info/software_versions.yml

Fixed

  • #697,#699,#713 - Template update for nf-core/tools version 2.13.1
  • #711 - From r207 and onwards Archaea sequences were omitted when parsing GTDB databases. (This did not affect sbdi-gtdb databases, only gtdb.)
  • #715 - Fix filtering vsearch clusters for high number of clusters
  • #717 - Fix edge case for sorting file names by using radix method
  • #718 - Require a minimum sequence length of 50bp for taxonomic classifcation after using ITSx
  • #721 - Fix error unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException caused by a missing \ in nf-core module pigz/uncompress (which had no consequences but was confusing)
  • #722 - When barrnap detects several genes select the lowest e-value
  • #726 - Add fallback to download_pipeline.yml because the pipeline does not support stub runs (#2846)

Dependencies

  • #720 - Updated nf-core modules, DADA2, and Phyloseq

| software | previously | now | | -------- | ---------- | ------ | | cutadapt | 3.4 | 4.6 | | DADA2 | 1.28.0 | 1.30.0 | | Phyloseq | 1.44.0 | 1.46.0 |

Removed

  • #710 - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0

Files

nf-core/ampliseq-2.9.0.zip

Files (1.7 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/ampliseq/tree/2.9.0 (URL)