All the single sample calling through to batch generation - these batches become custom cohorts, so this needs to be a separate precursor workflow.
Everything after that point - instead of running separate groupings as 'Cohorts', we can merge multisample 1 & 2 as a single massive workflow. The Multisample1 Stages remain as CohortStages, the Sandwich workflow and Multisample2 become MultiCohortStages.
Proposed Structure - simplest version is merging the Multisample 1 & 2 files into a single file, leaving the singlesample workflow as a separate script with its own stages, and keeping the common methods in a third file (for now, these are referenced in gCNV & GATK workflows, so maybe we should find a better naming convention/location)
Plan!
Proposed Structure - simplest version is merging the Multisample 1 & 2 files into a single file, leaving the singlesample workflow as a separate script with its own stages, and keeping the common methods in a third file (for now, these are referenced in gCNV & GATK workflows, so maybe we should find a better naming convention/location)