Release Ampliseq Version 2.9.0 · nf-core/ampliseq

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

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

#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)

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

#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)

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