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Add support for resetting operations with CWLTool

Marcel Loose requested to merge RAP-85_resetting-support into master

Add support for resetting operations with CWLTool.

When using Toil as CWL runner, it is possible to re-run parts of the pipeline by resetting one or more operations, using Rapthor's -r option. This merge request adds the possibility to also do this when using CWLTool as runner.

For each operation, the pipeline now writes a .done file into the working directory (e.g. in pipelines/calibrate_1) when the operation is completed. When the pipeline is re-run, all the operations that are marked as done are skipped.

Closes RAP-85

Edited by Marcel Loose

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