change stageInMode to copy and update module #25

Job	Run time
GPU \| parabricks/applybqsr \| docker_self_hosted \| 1	2m 7s
GPU \| parabricks/fq2bam \| docker_self_hosted \| 1	2m 4s
GPU \| parabricks/fq2bammeth \| docker_self_hosted \| 1	2m 2s
GPU \| parabricks/applybqsr \| singularity \| 1	3m 46s
GPU \| parabricks/fq2bam \| singularity \| 1	40s
GPU \| parabricks/fq2bammeth \| singularity \| 1	3m 55s
GPU \| parabricks/applybqsr \| docker_self_hosted \| 2	1m 49s
GPU \| parabricks/fq2bam \| docker_self_hosted \| 2	1m 48s
GPU \| parabricks/fq2bammeth \| docker_self_hosted \| 2	1m 50s
GPU \| parabricks/applybqsr \| singularity \| 2	3m 36s
GPU \| parabricks/fq2bam \| singularity \| 2	3m 42s
GPU \| parabricks/fq2bammeth \| singularity \| 2	3m 36s
	30m 55s

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