nf-core/ampliseq: Ampliseq Version 2.10.0

nf-core/ampliseq version 2.10.0 - 2024-06-27

Summary of changes

• added ANCOM-BC for differential abundance analysis
• updated reference databases for sbdi-gtdb & gtdb with R08-RS214-1 and R09-RS220, respectively
• template update 2.13.1 to 2.14.1
• several bug fixes

Detailed changes

Added

• #751 - Added version R08-RS214 of curated GTDB 16S taxonomy: sbdi-gtdb=R08-RS214-1 or sbdi-gtdb as parameter to --dada_ref_taxonomy
• #752 - Added version R09-RS220 of GTDB 16S taxonomy: gtdb=R09-RS220 or gtdb as parameter to --dada_ref_taxonomy
• #753, #756, #757 - ANCOM-BC via QIIME2 can be used with --ancombc, --ancombc_formula, and --ancombc_formula_reflvl, plotting can be modified with thresholds --ancombc_effect_size and --ancombc_significance

Changed

• #749 - Create barplot also when no metadata is given
• #753 - ANCOM via QIIME2 is not run anymore by default but on request whith --ancom, therefore --skip_ancom was removed

Fixed

• #747 - Template update for nf-core/tools version 2.14.1
• #748 - Updating misleading error message and documentation
• #750 - Numbers in overall_summary.tsv were fixed (sometimes misleading in 2.9.0 for columns "denoised[F/R]", "merged", and "nochim")

Removed

• #753 - --skip_ancom was removed