Software Enhancements - Githubissues

salvadorlab / mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

4 stars 1 forks source link

Software Enhancements #21

Closed noahaus closed 7 months ago

noahaus commented 10 months ago

[x] replace Roary (outdated) with panaroo
[x] test scoary functionality
[ ] revisit the implementation of coinfinder
[x] get rid of warning symbols with params values.

noahaus commented 10 months ago

[x] test panaroo output with scoary to see if it prints anything out

noahaus commented 10 months ago

panaroo is supposed to install simply, but is having issues being recognized. more confusingly, it will work with a minimal example but has trouble with the entire script.

Adding panaroo to the base mbovpan env with conda.

noahaus commented 10 months ago

panaroo is supposed to install simply, but is having issues being recognized. more confusingly, it will work with a minimal example but has trouble with the entire script.

Adding panaroo to the base mbovpan env with conda.

This seemed to do the trick - adds a lot of time however, but better than nothing 👍

noahaus commented 9 months ago

Now know how to filter the sequences, given that they are not M. bovis through the use of a python script that throws an exception if the output indicates a different M. bovis species