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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.
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Fix and generalize PAN mode #14

Closed noahaus closed 1 year ago

noahaus commented 1 year ago

I have to apply the changes that I worked on for improving pan mode

noahaus commented 1 year ago

The only things that are giving me a headache are gene_prab and accessory_pca. I was able to make progress to get the scripts themselves to start running, but now its going to be about integrating it back into the workflow.

Might be easier just to have these two things be helper scripts - will explore tomorrow

noahaus commented 1 year ago

Decided to remove the processes - it was too difficult to rectify the commands in the nextflow script and my R script. That being said, I will need to make sure the individual scripts work when called upon now. Will close this issue but open another in its place