aidenlab
juicer version for Snakemake?
Is there such one or anyone working on re-coding?
Snakemake implementation would solve the platform dependence. There would be then a single workflow/Snakefile that can be run with various platform configurations (SLURM/LSF/singleCPU).
Seems like an interesting idea! No one is working on snakemake to my knowledge, although ENCODE does have a repo that uses wdl. (which seems similar / might be easier to port from?) https://github.com/ENCODE-DCC/hic-pipeline
Thank you! Yes, they have the WDL encoded workflow and even some docker images to use in it, may be useful.
I've played a bit with the primary processing part, coded it up to the reduplicated BAM file in snakemake, but now test normal, full juicer runs. Maybe when I have more confidence in understanding juicer results can extend my snakemake workflow and share with you...