add tool: integron finder 2.0 - Githubissues

fmalmeida / bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

https://bacannot.readthedocs.io/en/latest/

GNU General Public License v3.0

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add tool: integron finder 2.0 #50

Closed fmalmeida closed 1 year ago

fmalmeida commented 2 years ago

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.

fmalmeida commented 1 year ago

Mentioned as a request in #78

fmalmeida commented 1 year ago

To make things easier to maintain, should be tackled together with #69

fmalmeida commented 1 year ago

Progress update:

[x] Tool module added
[x] Results parsed and merged to final GFF
[x] Results parsed and added to JBrowse
[x] Results parsed and added to HTML reports
[x] Add to JSON summary

fmalmeida commented 1 year ago

Seems to be ready for merging in dev. Needs to pass tests.

fmalmeida commented 1 year ago

It is working properly. Needs to update docs and changelog before merging to dev.

fmalmeida commented 1 year ago

also working with singularity ... it is ready to merge

fmalmeida commented 1 year ago

Tool added in dev branch 🥳