Gracefully handle low depth samples with StarPhase/PharmCAT

[williamrowell]

• Remove StarPhase outputs that are not allowed as PharmCAT input (Feature request: PharmCAT accepts no-call result from outside call file PharmGKB/PharmCAT#204)
  • NO_READS is used in StarPhase output to indicate no-calls.
  • NO_MATCH is used when StarPhase can't match the variants to a known allele.
  • This workaround removes NO_READS/NO_MATCH outputs.
• Only attempt to run PharmCAT if at least one PharmCAT region has depth > pharmcat_min_coverage

[holtjma]

I think a lot of these files were just whitespace shifting, the wdl_common file looks fine though