Make 0.setup.R agile to config.yml

[HenrikBengtsson]

Creating a new issue based on the below:

@ivan108 wrote:

I wonder what does it take to move that path into config.yml?

@HenrikBengtsson replied:

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

[HenrikBengtsson]

So, I completely forgot that there already was config.yml file in this project; I read your initial comment as a request to add a config.yml file.

After re-reading, I now take it as you wanted 0.setup.R to be agile to whatever is in the config.yml file. Maybe we could add support for that.

If I recall it correctly, the main purpose of the 0.setup.R file was to programmatically "communicate" what the intent of the different folders is instead of trying to cover it all in the documentation. I'll add it to the wish list.

[HenrikBengtsson]

@ivan108 wrote:

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?

Yes, it makes sense to at least keep config.yml and 0.setup.R consistent this way.

PS. Maybe this adds another argument for making 0.setup.R follow whatever is set in config.yml.

[ivan108]

Yes, that was my original thought, since we already have config.yml, why not to use it in the 0.setup.R, instead of hard coding...