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Remove input read indices, make reference index optional and combine same sample together #133

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Remove input read indices, make reference index optional and combine same sample together

Remove input read indices, make reference index optional and combine same sample together #133

Run time

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Job Run time
Run pipeline with test data (22.10.1)
4m 41s
Run pipeline with test data (latest-everything)
4m 12s
8m 53s