2.99.3 Primers
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)
-
frameshift_deletions_checks
: report on stop codons
Bug fixes:
- correctly compute runtime requirement within groups
Preview feature:
- first re-introduction of benchmarking features since V-pipe 2.0
see: resources/auxiliary_workflows/benchmark/
Documentation:
- Improved tutorial available inside subdirectory docs/
- V-pipe now relies on snakemake 7.11 to properly handle 'runtime' resource. Consider upgrading !
- by default the samples' tables
coverage.tsv.gz
andbasecnt.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