fmalmeida/bacannot: A pipeline for an easy but comprehensive annotation of prokaryotic genomes

Changes Some minor but important changes have been made. Manuals Variable names adjusted in the documentation Prokka Prokka annotation process does not accept anymore an option to give the institution name since it renames the contigs for a pattern that inhibits JBrowse from running Nanopolish Nanopolish have been updated to exactly follow the instructions under the manual calling only CpG methylations which makes the pipeline run faster JBrowse JBrowse have been updated to the latest version, 16.9, make sure to use the right JBrowse Desktop version CARD-RGI rgi annotation pipeline have been updated to run only using BLAST since DIAMOND was running through a lot of errors due to its databases. This however made differences in the output format (you have to check it wisely). Reports Finally, html reports have been updated to match all these changes.Please do not download the files via Zenodo since it does not keep track of minor changes. Get the latest pipeline release docs via Github or Nextflow