nf-core/ampliseq: Ampliseq Version 2.2.0

nf-core/ampliseq version 2.2.0 - 2022-01-31 Summary of changes

• Added features (e.g. SBDI-GTDB db update, Adonis test)
• Added convenience updates (e.g. properly reporting and on demand ignoring low read samples)
• Updated to nf-core template 2.2
• Fixed some bugs

• #352, #372 - --skip_dada_addspecies allows to skip species level classification to reduce memory requirements, incompatible with --sbdiexport that expect species annotation.
• #364 - Adonis in QIIME2 for testing feature importance in beta diversity distances, --qiime_adonis_formula can be set to provide a custom formula.
• #366 - New version of the SBDI-GTDB taxonomy database: v. 3. (Fixes problem with Reverse_ added to some domain strings.)

• #354 - Input files and files after primer trimming with cutadapt are required to be >1KB (i.e. not empty) and either the pipeline will stop if at least one sample file fails or the failing samples will be ignored when using --ignore_empty_input_files or --ignore_failed_trimming, respectively.
• #376 - Forbid sampleIDs starting with a number when also --metadata is used, because such strings are unintentionally modified and the metadata will not match any more.

• #377- An error message will occur when --sbdiexport is used with --skip_taxonomy or --skip_dada_addspecies
• #375- Updated documentation regarding not using curly brackets in --extension with --single_end
• #362- Template update for nf-core/tools version 2.2, now requires nextflow version >= 21.10.3
• #374- Cutadapt results can be now also viwed in the MultiQC report

• #350 - Remove redundant derepFastq step (has no impact on results)