Ampliseq Version 2.11.0

nf-core/ampliseq version 2.11.0 - 2024-08-06

Summary of changes

This update is mostly about reference taxonomy databases:

• added reference databases sbdi-gtdb=R09-RS220-1 for DADA2
• added reference databases unite-fungi=10.0 and unite-alleuk=10.0 for SINTAX
• disabled UNITE reference databases for QIIME2
• fixed broken urls for UNITE databases

Detailed changes

Added

• #765 - Added version R09-RS220 of curated GTDB 16S taxonomy: sbdi-gtdb=R09-RS220-1 or sbdi-gtdb as parameter to --dada_ref_taxonomy
• #766 - Added version 10 of Unite as parameter for --sintax_ref_taxonomy: unite-fungi=10.0 and unite-alleuk=10.0

Changed

• #762 - Improved output documentation section "Optional ASV filtering" and parameter documentation
• #766 - Modified warning filenames from QIIME2_ANCOM to avoid collisions
• #766,#769 - Disabled Unite databases from the --qiime_ref_taxonomy because of divergent results compared to the other classifiers

Fixed

• #761 - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0
• #766 - Fixed broken urls for Unite databases (issue #764)
• #769 - Reference taxonomy database values were not properly validated in versions 2.9.0 and 2.10.0