approach 2 to issue #29

[Layth17]

Approach 2

[malachig]

One thing about this solution. What will be the final file name of the result file that is saved? It looks like it might just be a generic name? I think we need some way to make this come out in a way that the end user can clearly distinguish between the tumor and normal optitype results

[malachig]

Yeah currently in the final result we get normal results here:
hla_typing/optitype_result.tsv

And tumor results at the top level
optitype_result.tsv

Can we instead reorganize the outputs so that these are in:
hla_typing_normal/
hla_typing_tumor/

[malachig]

Looks good to me. Tested with Layth and the results looked good as well.