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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
402 stars 180 forks source link

juicer version for Snakemake? #289

Open michalogit opened 1 year ago

michalogit commented 1 year ago

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).

sa501428 commented 1 year ago

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

michalogit commented 1 year ago

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...