Roll config file into command line parameters?

[oneillkza]

Right now half of the parameters to Talon are passed directly (e.g. --db, --build), but the other half (sample info, sam file) are passed via a separate comma-separated file. This is a little fiddly for running Talon in a broader workflow, and also seems unnecessary.

Would it be possible to make the four fields in the csv be their own named parameters?

e.g. something like:

--f SAM_FILE
--dataset 
--sample_descr
--platform

[fairliereese]

Same with this one, I agree that this would be nice and I will try to roll this into the next big update!

Edit: For the record, it works this way to support easily running TALON on multiple input SAM files at a time!