Felipe Marques de Almeida
Felipe Marques de Almeida
## PR checklist Adding Shasta assembler module Closes #1185 - [x] If you've added a new tool - have you followed the module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md) - [x]...
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
This PR will host modifications required to add an option to run `bakta` instead of `prokka` for primary annotation if desired.
Study the best way to implement [Bakta](https://github.com/oschwengers/bakta) in the pipeline. It will be nice to provide the users with the option to choose the base annotation with Prokka or Bakta,...
Would be good if possible to add a new tool for prophage annotation: https://github.com/gbouras13/pharokka
A new tool for the annotation and indentification of Integrons in Bacteria has been made available: https://github.com/gem-pasteur/Integron_Finder Would be super nice to have it incorporated in the analysis.
Add to the pipeline the new tool called [f5c](https://github.com/hasindu2008/f5c) which is a reimplementation of `Nanopolish` and is much faster. Add this tool, but not replace nanopolish. Instead, make the pipeline...
Add an additional module for scanning the sample using [sourmash](https://github.com/sourmash-bio/sourmash): - [x] scan against refseq using whole genome (LCA) - [x] an option to create a simple phylogeny using sourmash...
Add a step to create a additional AMR report with https://github.com/pha4ge/hAMRonization tool, which enables a nice way to visualise and compare the results between AMR tools.
This brings forward the feature request that was first discussed at: * #35 Since the issue was not related to it and is now closed, it was necessary to open...