running germline separately and without running somatic analysis in the same project run may be necessary for the following reasons:

• normal samples are often consented asynchronously from their tumor counterparts, and normal samples cannot be run until they are consented
• currently germline mode automatically turns on somatic mode, so running germline analysis on an ad hoc basis will produce a second set of somatic results if somatic mode was already previously generated.

One option is to use a separate input stream (for example --germline <file with sample names> so we can use it in the wes_repo run. however, we would have to maintain this list up-to-date to keep up with PartC changes, which might be a challenge because PartC consent is not maintained in the lims. the other option is add an additional entry point for germline analysis that allows us to point to previously generated somatic results. It could look like --germline <file> where columns are:

TUMOR_ID	PATH
s_C_TUMORX_T001_d	/path/to/results

files required from somatic samples include facets output in the channel facetsForMafAnnoGermline, and the somatic bam. the latter can be provided with the --mapping/--bamMapping options.