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NCI-CGR / plco-analysis

Primary workflow for the PLCO "Atlas" project
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clean up Makefile.config #8

Closed lightning-auriga closed 3 years ago

lightning-auriga commented 3 years ago

Makefile.config is one of the single oldest pieces of the pipeline. it's being used, no question; but it has an accumulated pile of garbage in it. of the various things to go through and clean up before departure, this is probably the highest priority. notably, it still has enumerated extension definitions in it when those are now being primarily handled in a yaml file along with https://github.com/NCI-CGR/initialize_output_directories, so it's actually quite bad.

lightning-auriga commented 3 years ago

other major potential issue is whenever something isn't currently in Makefile.config but rather hard-coded into the individual pipelines once or particularly multiple times. that needs to get fixed immediately.

lightning-auriga commented 3 years ago

this is pretty much as good as it's going to get under my limited time remaining