Published May 23, 2025 | Version 2.14.0
Software Open

nf-core/ampliseq: Ampliseq Version 2.14.0

Creators

  • 1. Quantitative Biology Center (QBiC)
  • 2. National Bioinformatics Infrastructure Sweden (NBIS)
  • 3. Linnaeus University & Stockholm University
  • 4. Boehringer Ingelheim
  • 5. PeriMatrix IT Consultancy
  • 6. Minderoo Foundation
  • 7. @NBISweden
  • 8. Lund University
  • 9. QBiC @qbicsoftware
  • 10. HUJI
  • 11. @seqeralabs
  • 12. Data Science Centre, EMBL
  • 13. @FredHutch
  • 14. Analysis and Bioinformatics for Marine Science (ABiMS)
  • 15. Seqera
  • 16. STFC Hartree Centre
  • 17. Seqera Labs
  • 18. CNRS, Station Biologique

Description

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

Files

nf-core/ampliseq-2.14.0.zip

Files (1.7 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/ampliseq/tree/2.14.0 (URL)

Software

Repository URL
https://github.com/nf-core/ampliseq