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Fix paired end sample handling #1018

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Fix paired end sample handling

Fix paired end sample handling #1018

Run time

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Job Run time
Run pipeline with test data (1, 23.10.4, docker)
7m 25s
Run pipeline with test data (1, 23.10.4, docker)
19m 57s
Run pipeline with test data (1, 23.10.4, docker)
22m 26s
Run pipeline with test data (1, 23.10.4, docker)
22m 8s
Run pipeline with test data (2, 23.10.4, docker)
1m 25s
Run pipeline with test data (2, 23.10.4, docker)
10m 4s
Run pipeline with test data (2, 23.10.4, docker)
10m 4s
Run pipeline with test data (2, 23.10.4, docker)
10m 17s
Run pipeline with test data (3, 23.10.4, docker)
4m 58s
Run pipeline with test data (3, 23.10.4, docker)
5m 20s
Run pipeline with test data (3, 23.10.4, docker)
6m 56s
Run pipeline with test data (3, 23.10.4, docker)
5m 45s
Run pipeline with test data (4, 23.10.4, docker)
1m 5s
Run pipeline with test data (4, 23.10.4, docker)
7m 20s
Run pipeline with test data (4, 23.10.4, docker)
5m 54s
Run pipeline with test data (4, 23.10.4, docker)
5m 40s
2h 26m 44s