Add bam/cram support #349

Job	Run time
Test pipeline \| docker \| 24.04.2 \| 1/5	25m 31s
Test pipeline \| docker \| 24.04.2 \| 1/5	25m 31s
Test pipeline \| docker \| 24.04.2 \| 2/5	9m 59s
Test pipeline \| docker \| 24.04.2 \| 2/5	10m 2s
Test pipeline \| docker \| 24.04.2 \| 3/5	18m 55s
Test pipeline \| docker \| 24.04.2 \| 3/5	13m 22s
Test pipeline \| docker \| 24.04.2 \| 4/5	12m 42s
Test pipeline \| docker \| 24.04.2 \| 4/5	15m 0s
Test pipeline \| docker \| latest-everything \| 1/5	11m 8s
Test pipeline \| docker \| latest-everything \| 1/5	11m 8s
Test pipeline \| docker \| latest-everything \| 2/5	10m 11s
Test pipeline \| docker \| latest-everything \| 2/5	11m 9s
Test pipeline \| docker \| latest-everything \| 3/5	12m 55s
Test pipeline \| docker \| latest-everything \| 3/5	11m 34s
Test pipeline \| docker \| latest-everything \| 4/5	13m 36s
Test pipeline \| docker \| latest-everything \| 4/5	12m 23s
	3h 45m 6s

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