Currently, LoFreqSomatic implements a "callerType" value, whereas MuTect2 implements "chunkLabel". LoFreqSomatic's "callerType" ends up getting passed in to the "chunkLabel" channel variable. This causes problems where its not possible to differentiate between MuTect2 chunk labels and LoFreqSomatic caller types downstream, including the latter being absent from the final annotation table.
Need to refactor the output channels for paired steps to include both "callerType" and "chunkLabel", and refactor all downstream processes that use them with this new cardinality.
Currently, LoFreqSomatic implements a "callerType" value, whereas MuTect2 implements "chunkLabel". LoFreqSomatic's "callerType" ends up getting passed in to the "chunkLabel" channel variable. This causes problems where its not possible to differentiate between MuTect2 chunk labels and LoFreqSomatic caller types downstream, including the latter being absent from the final annotation table.
Need to refactor the output channels for paired steps to include both "callerType" and "chunkLabel", and refactor all downstream processes that use them with this new cardinality.