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Remove input read indices, make reference index optional and combine same sample together #136

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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 #136

Run time

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Job Run time
Run pipeline with test data (22.10.1)
5m 33s
Run pipeline with test data (latest-everything)
4m 28s
10m 1s