Remove code duplication in main workflow

VIB-PSB / MINI-AC

Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants

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Remove code duplication in main workflow #3

Closed hdbeukel closed 11 months ago

hdbeukel commented 1 year ago

I removed the duplication from the main workflow. Species id is now determined first and then used to compose the input file paths. I still have some questions before we can merge this, see below.

hdbeukel commented 12 months ago

TODO:

[x] update documentation in [yourdocs/configuration_pipeline.md for renamed motif mapping file params

nicomaper commented 11 months ago

Thanks, Herman, for working on this code reduction! All the changes seem fine to me, and also I trust the test, so I don't worry too much about whether they can alter the code ;) thanks to the changes, now it is much more clean and it will be much easier to add new species or new genomes.