Writes pheno-specific output to a provided path

[MattWellie]

Fixes

• Currently we pass one path, write a file to that path, then maybe write a second file to a modified version of that path
• in hindsight, a stupid idea
• This means that the pipeline-run version of AIP is generating both files, but doesn't know to copy the second file out of the job, so we're not generating phenotype-specific seqr files

Proposed Changes

• adds two CLI arguments, one for each file