nf-core/ampliseq version 2.14.0 - 2025-05-23 Summary of changes Multi-region analysis is now easier with custom databases, parameters were changed or added Updated sbdi-gtdb, gtdb, PR2 databases and added BOLD plant databases for classification with DADA2 Follow nextflow's strict syntax (only impacts development) Detailed changes Added #879 - Add sbdi-gtdb=R10-RS226-1 as parameter to --dada_ref_taxonomy and make this version the default for sbdi-gtdb. #882 - Add gtdb=R10-RS226 as parameter to --dada_ref_taxonomy and make this version the default for gtdb. #883 - Add BOLD databases plantae-bold-its1 & plantae-bold-trnL, for plant samples with markers ITS1 and trnL, versions 20240510, for DADA2 as parameter to --dada2_ref_taxonomy. #885 - Add pr2=5.1.0 as parameter to --dada_ref_taxonomy and make this version the default for pr2. Changed #871 - Multi-region analysis is now easier with custom databases. No alignment file of the reference sequences are needed. | Parameter | Description | | ------------------------- | ------------------------------------------------------------------------------------------------------- | | sidle_ref_tax_custom | Changed: Previously three files, now one file: path to reference taxonomy strings | | sidle_ref_seq_custom | New: Path to reference taxonomy sequences in fasta format | | sidle_ref_aln_custom | New: Path to multiple sequence alignment of reference taxonomy sequences in fasta format | | sidle_ref_degenerates | New: Only effective with --sidle_ref_tax_custom, filter reference sequences, default: 5 | | sidle_ref_cleaning | New: Arguments regarding ad-hoc cleaning, with --sidle_ref_tax_custom default is '--p-database silva' | Fixed #872 - Follow nextflow's strict syntax #876 - Pulled the updated vsearch/clusters module from nf-core to fix a bug where a wildcard expansion trigging an arguments-too-long error. #878 - Downgraded nf-schema from 2.3.0 to 2.2.0 due to incompatibilities with nextflow stable versions 25.05 and newer #881 - Template update for nf-core/tools version 3.2.1 #887 - Updated documentation to include all updates