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HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data
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Fixed path #17

Closed ivan108 closed 5 years ago

ivan108 commented 5 years ago

New path for Costello exome data on the cluster

ivan108 commented 5 years ago

I hope I did it right?

HenrikBengtsson commented 5 years ago

You certainly did. Thxs.

PS. If you inspect what I did on my end, I ended up merging your PR to the develop branch instead, then basically merged that into a master, add git tag '0.4.2', and pushed the new "release" 0.4.2. I took this detour because that is how I do all my releases elsewhere.

ivan108 commented 5 years ago

OK, thanks! I wonder what does it take to move that path into config.yml ?

HenrikBengtsson commented 5 years ago

One easier, quicker approach is to be able to override the default via an env var. See ?Sys.getenv.

ivan108 commented 5 years ago

Quick question, in default config.yml file the "dataset" is defined as "CostelloP_2015-Exome,bwa,realigned,rmDups,recal" and in 0.setup.R the "path" is defined as "bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/". So if I change dataset name, shall I also change "path" or it doesn't matter? Thx