Tags

Fix tRNAs/5S parsing after bakta update

force output dir for bakta and explicit column names in check_tRNA

bump bakta version v.1.9.3 and update database

Fix empty plasmid file

Concatenate genome and plasmids sequences (if any). Add plasmids proteins annotations

Update snakemake wrappers to fix conda

Better checksums; output table and unpaired reads can be included

Fix conda environments after version bump

Fix metaxa version typo

Better documentation and version bumps for bakta

as well as others minor bumps for checkm, metaxa2 and SPades

Recovered the behavior of length of 0bp when LSU/SSU/plasmids are not detected

Fix issue in plasmid length summary. No compliant mode

Lengths in summary, min 500bp contigs and no MDMcleaner, plus fixes

Handle exceptions from MDMcleaner. Fix plasmid workflow to not trigger unneeded rules.

Fix IndexError issue with input function

Fix bugs such as issue with Recycler failing with unconnected plasmid assembly graph or missing gene names in annotations. Add assembly date and workflow version to the summary table. Better documentation regarding the rerun behavior of Snakemake

Bakta v1.5 at least

Reduce disk space with new temporary files

Better READMEs; plasmids when needed; 0-bp LSU/SSU if not detected

The assembly quality assessment is performed to evaluate the compliance to the SeqCode and the MIMAG