Started moving code from WorkflowRunnerVersion2 to multiple example classes
Maybe we do not need the WorkflowRunner class at all. The different WorkflowEngine and Workflow implementations provide enough functionality to run workflows. Some examples are useful to see how these classes can be used.
- Copied code from the WorkflowRunnerVersion2 class to the ConcatenateExample and BaseExample classes.
- RemoveFirstAndBeginningExample: started work on a third simple workflow example that will have parameters (it removes a number of lines from the input file and removes a number of characters from the start of all remaining lines).
- GalaxyWorkflowEngine: the mapping (for input files) from generic names to Galaxy labels in the prepareWorkflow method now works again for example workflows 1 and 2.
- FileUtils: the createInputFile method can now handle multiple lines.