fmalmeida/bacannot: fmalmeida/bacannot v2.4

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

This release marks the incrementation of the pipeline with two more modules:

1. A new module for the annotation of secondary metabolites with antiSMASH has been added.
   • The modules runs only with antiSMASH core modules in order to keep it fast
   • This step can be skipped with --skip_antismash
2. A new plugin has been added to the Web (Shiny) App. SequenceServer has been implemented inside the app so that users can quickly execute and visualise blast alignments against the samples' genome, genes and proteins.

Also, a small fix was performed in the run_jbrowse.sh script. To add the antismash results and to properly check whether digIS results are available or not.

Finally, a small fix in the merge annotation process and SQLparser in the shiny app was also performed to include Resfinder as an option.

Because of that:

• The fmalmeida/bacannot:server has been updated
• A new image fmalmeida/bacannot:antismash is now available for antiSMASH module