Ampliseq Version 2.14.0

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