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Ampliseq Version 2.9.0

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@d4straub d4straub released this 03 Apr 13:29
2.9.0
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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
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