bacannot
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fmalmeida
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
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.
Hey Felipe, Building upon the stylistic change suggested in https://github.com/fmalmeida/bacannot/issues/38 Perhaps instead of using the `prokka.out[1]` etc, we can rely upon named outputs ```nextflow annotations_files_ch = (PROKKA.out.renamed_genome).join(PROKKA.out.gffAnnotation) .join(MLST.out.mlstAnalysis) .join(BARRNAP.out.gffTuple) ```...
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...
**Describe the bug** Bugs occurred when annotating custom database, that **table in report** files are EMPTY, although **annotiation summary** files NOT EMPTY. **To Reproduce** Steps to reproduce the behavior: 1....
