fixing vcfProcessLog and TUMOR/PRIMARY issue

[jacmarjorie]

This PR handles vcfProcessLog and TUMOR/PRIMARY issue globally.

I am also suggesting (as this was the cleanest way to proceed with vcfProcessLog) to remove the need for the tcga-reheader-config file creation. If these values can all be passed into vcf reheader without disrupting any flow then this is the best option. All values would be satisfied via the "manual" selection within vcf reheader config tool.

If we agree, I can do some basic clean up on this branch before merging.

Outstanding issues at this point:

• [x] GL
• [x] provide date in correct format yyyyMMdd
• [x] softwareParam incompatibility: https://github.com/ucscCancer/mc3/issues/1
• [ ] set all values in .ga file to satisfy tool level variables

[jacmarjorie]

@kellrott can you test and accept this on your end. In the mean time, I can add the parameters to the galaxy workflow in the mc3 repo.