change stageInMode to copy and update module #23

Job	Run time
GPU \| parabricks/applybqsr \| docker_self_hosted \| 1	1m 43s
GPU \| parabricks/fq2bam \| docker_self_hosted \| 1	1m 52s
GPU \| parabricks/fq2bammeth \| docker_self_hosted \| 1	2m 5s
GPU \| parabricks/applybqsr \| singularity \| 1	3m 48s
GPU \| parabricks/fq2bam \| singularity \| 1	37s
GPU \| parabricks/fq2bammeth \| singularity \| 1	34s
GPU \| parabricks/applybqsr \| docker_self_hosted \| 2	1m 39s
GPU \| parabricks/fq2bam \| docker_self_hosted \| 2	1m 46s
GPU \| parabricks/fq2bammeth \| docker_self_hosted \| 2	1m 40s
GPU \| parabricks/applybqsr \| singularity \| 2	3m 47s
GPU \| parabricks/fq2bam \| singularity \| 2	34s
GPU \| parabricks/fq2bammeth \| singularity \| 2	34s
	20m 39s

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