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open2c / quaich

snakemake pipeline for Hi-C post-processing
MIT License
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view usage/verification #7

Open gfudenberg opened 1 year ago

gfudenberg commented 1 year ago

would it make sense to verify view/cooler compatibility before launching all rules?

also, did we decide that views should be saved w/o headers?

it seems that many rules don't support views-- should that be a future upgrade?

Phlya commented 1 year ago

Re verification, that's a good idea.

Headers - I don't know... Good question.

All rules support a view (where the underlying command supports it, so not chromosight or mustache), just define it once at the top of the config and it will be applied everywhere.

Phlya commented 1 year ago

Verification is done! Just in the main code in the Snakefile for local coolers, and immediately in the download rule for remote coolers.

Phlya commented 1 year ago

In general there are a lot more checks that con be done on all inputs, we can just start a separate issue with a checklist for that.

Phlya commented 1 year ago

~FYI actually for now I disabled this because for some reason it was erroring on valid views... Need to figure it out at some point.~ Actually, seems fine...

Phlya commented 1 year ago

After all I keep getting errors for view that are totally valid, no idea why....