This is effectively a fork of FitHiC2, converted to a nextflow pipeline, using the guidelines described in the Nature Protocols manuscript.
Main changes:
- Uses JuicerTools to dump the interactions, and perform the normalisation
- Modified the CombineNearbyInteraction.py script to pre-cluster neighbouring bins, vastly improving the run time for high resolution data
- make Docker/singularity of fithic rather than conda