Added parameters for EdgeR DGE workflow
- fdr, output_format_images, and outputs parameters were added.
Fixed some bugs and adjusted for new Galaxy API
- ConcatenateExample: fixed bug in runExample method (result = false) after feedback during DTL programmers meeting!
- RnaSeqDgeExample: set fdr, output_format_images, and outputs as parameters (instead of input files).
- GalaxyWorkflowEngine: check step index before using it in the createInputsObject method.
- HistoryUtils: remove old file if it exists, directly download the dataset according to the new Galaxy API, and removed the data type parameter in the downloadDataset method, check for null references in the downloadFileFromUrl method.
- Constants: added URL for Galaxy at Vancis, renamed GALAXY_INSTANCE_URL to CENTRAL_GALAXY_URL, renamed TRAIT_GALAXY_INSTANCE_URL to SURF_SARA_GALAXY_INSTANCE_URL, and renamed TEST_WORKFLOW_CONCATENATE to CONCATENATE_WORKFLOW.