nf-core/ampliseq: Ampliseq Version 2.17.0

nf-core/ampliseq version 2.17.0 - 2026-04-15

Summary of changes

• sample sheet standardization (legacy sample sheet still allowed)
• added Decontam for decontamination
• added ITSxRust alongside ITSx
• improved phylogenetic placement
• data handling optimization for binned quality sequencing data
• local storage for reference databases
• a bunch of bug fixes

Detailed changes

Added

• #948,#976 - Decontam as optional decontamination tool.
• #949 - The dataset can be filtered for downstream analysis with the metadata sheet, for example to remove negative control samples meant for Decontam.
• #959 - Add the possibility to place ASVs in the best matching tree through a spreadsheet with HMM profiles and corresponding reference trees (see usage doc).
• #959 - Add archaeal and bacterial reference trees for phylogenetic placement to sbdi-gtdb reference database (see usage doc; only for the current release, i.e. R10-RS226-2).
• #957,#979 - Added ITSxRust as an optional alternative to ITSx for ITS region extraction via --its_extractor itsxrust.
• #964,#968 - Enabled local reference storage directory with --ref_taxonomy_storage.
• #972 - Amended information about merging in the overall_summary.tsv and the summary report.
• #978 - --binned_quality (string, comma separated quality bins) uses DADA2's built-in function to handle quality binned fastq data.
• #981 - Standardized sample sheet column names to match nf-core conventions (legacy sample sheet is still valid)
• #982 - Adds --sintax_ref_tax_custom and --sintax_assign_taxlevels.

Changed

• #960 - Export beta diversity distance matrix in tsv format.
• #983,#985 - Update documentation

Fixed

• #952 - Ensure paired FASTQ files stay aligned by generating reverse paths from forward files instead of sorting independently
• #958,#970,#971 - Fix AWS tests
• #966 - In multiregion analysis, omit samples with few reads across all regions
• #969 - Fix checking for sbdiexport compatibility for newer nextflow versions
• #984 - Adhere to strict syntax, incl. update to nf-core modules
• #986 - Update database links from https://scilifelab.figshare.com/ndownloader/files/ to https://ndownloader.figshare.com/files/ to alleviate download issues.
• #989 - Execute downstream analysis when using --classifier.

Dependencies

• #977 - Updated DADA2 1.34.0 to 1.38.0

| software | previously | now | | -------- | ---------- | ------ | | decontam | | 1.30.0 | | DADA2 | 1.34.0 | 1.38.0 |

Removed

• #978 - --illumina_novaseq (boolean) was replaced by --binned_quality (string)