This PR addresses the pipeline changes needed to meet a user request to re-align the consensus genome to the reference to aid in identification of INDELS. The realignment step is already performed in the RunMinion step for ONT data, but was not performed for Illumina data. This PR exposes the existing results for ONT and adds a new step to generate the results for Illumina data.
The results will not be available to users with this PR - that would require additional work on the web side to make the results available.
This PR addresses the pipeline changes needed to meet a user request to re-align the consensus genome to the reference to aid in identification of INDELS. The realignment step is already performed in the RunMinion step for ONT data, but was not performed for Illumina data. This PR exposes the existing results for ONT and adds a new step to generate the results for Illumina data.
The results will not be available to users with this PR - that would require additional work on the web side to make the results available.