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Revert "Resolve RAP-224 "Avoid copies""

Marcel Loose requested to merge RAP-303_Fix-WorkflowException into master

This reverts commit c82a3a4f.

The use of InplaceUpdateRequirement is probably unnecessary to avoid copies (TBC), and its introduction caused WorkflowException issues, because in-place updated data were not specified as outputs. The thing is that these inputs will not be updated at all by the different workflows, so the use of InplaceUpdateRequirement is not really suitable here.

Toil should not create copies of read-only inputs, and AFAIK it doesn't. It creates symbolic links. However, since @rafferty reported that unwanted copies are being made, this should be investigated further.

Closes RAP-303

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