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2.99.3 Primers

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@DrYak DrYak released this 02 Nov 16:03
· 371 commits to master since this release

New features:

  • primer trimming using iVar (by default) or samtools

  • per sample primer protocol using new 4-column sample.tsv format (e.g.: for long running projects where protocols change to adapt to new variants)

    see: config/README.md#amplicon-protocols

  • frameshift_deletions_checks: report on stop codons

Bug fixes:

  • correctly compute runtime requirement within groups

Preview feature:

Documentation:

  • Improved tutorial available inside subdirectory docs/

⚠️ Breaking changes:

  • V-pipe now relies on snakemake 7.11 to properly handle 'runtime' resource. Consider upgrading !
  • by default the samples' tables coverage.tsv.gz and basecnt.tsv.gz are now 1-based: the first position of the genome is named '1' (as standard with genome notations, as in tools like samtools, and as used in formats like VCF)
    This can be switched back to 0-based (numbering starts at 0, as in python tools like PySAM, and as in the BED format) in config file, in section general option tsvbased