Pipeline remodelling. Issues 24, 31 and 36 - 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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Pipeline remodelling. Issues 24, 31 and 36 #44

Closed fmalmeida closed 2 years ago

fmalmeida commented 2 years ago

The implementation is not ready yet. This PR has been opened just to better keep track of changes made.

fmalmeida commented 2 years ago

Next steps:

Fix the download, formatting and usage of (blast) databases:
- [x] ICEberg
- [x] PHAST
- [x] VFDB
- [x] Victors
- [x] ARGminer and prokka table in resistance report
- [x] Custom databases
[x] Re-check the final GFF annotation to see whether the information about the databases are being added correctly and standardized.
[x] Check JBrowse output
[x] Check bacannot server

fmalmeida commented 2 years ago

Everything seems to be working properly ... Must now work on updating the documentation and making sure everything is thoroughly explained. Also, ensure that docker images are available. Must check:

[x] Is it running with singularity?

fmalmeida commented 2 years ago

It passed the tests with singularity. Just need to:

[ ] Update docs
[ ] Update github testing workflow to meet new design

fmalmeida commented 2 years ago

Not being able to run the tests in git action due to disk space (databases and docker images together consume more than what is available).

However, local tests with singularity and docker have passed.

Just need to update documentation for these new implementations.