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Ampliseq Version 2.6.0
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@d4straub d4straub released this 27 Jun 07:09
· 716 commits to master since this release
2.6.0
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nf-core/ampliseq version 2.6.0 - 2023-06-27

Summary of changes

  • Updated taxonomic databases (UNITE 9.0, PR2 5.0.0)
  • Added more choice for taxonomic classification: phylogenetic placement, SINTAX
  • Codon usage based filtering allows for additional QC of coding regions
  • Add NF-TEST pipeline end-to-end tests for existing CI tests
  • nf-core template update from 2.7.2 to 2.8

Detailed changes

Added

  • #564,#567,#582 - Added phylogenetic placement
  • #577 - Added SINTAX for taxonomic classification
  • #575, #586 - Added filtering step for stop codons for ASVs that are of coding regions.
  • #580 - Add NF-TEST pipeline end-to-end tests for existing CI tests
  • #591 - New version of the Unite taxonomy databases: 9.0
  • #596 - New version of the PR2 taxonomy database: 5.0.0, only available with DADA2 (--dada_ref_taxonomy)
  • #597 - Samples with less reads than specified with --min_read_counts (default: 1) stop the pipeline, previously the threshold was 1KB in size.

Changed

  • #563 - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
  • #567 - Renamed --dada_tax_agglom_min and --qiime_tax_agglom_min to --tax_agglom_min and --dada_tax_agglom_max and --qiime_tax_agglom_max to --tax_agglom_max
  • #580 - GitHub Actions CI - pull_request to dev tests with NXF_VER latest-everything & pull_request to master tests with NXF_VER 22.10.1 & latest-everything
  • #598 - Updated Workflow figure with SINTAX and phylogenetic placement
  • #599 - For exact species assignment (DADA2's addSpecies) PR2 taxonomy database (e.g. --dada_ref_taxonomy pr2) now excludes any taxa that end with " sp.".

Fixed

  • #553 - Handle empty barrnap results files
  • #554 - Accept taxonomy strings that contain #,'
  • #569 - Make header of overall_summary.tsv consistent between input data types
  • #573 - Avoid parser error for single-end data when an empty read file is detected
  • #578 - Template update for nf-core/tools version 2.8, including changing System.exit(1) to Nextflow.error()
  • #594 - Update metadata documentation
  • #595 - Closing gaps in rarefaction depth for diversity calculations (mindepth in QIIME2_DIVERSITY_CORE)
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