These are the Galaxy Workflow files that define the MIRACUM pipeline used in Galaxy. To use these workflows, import the files into any Galaxy instance that has all required tools installed, then run the Miracum - main, Miracum - variant annotation and Miracum - report variants workflows (or their panel counterparts), in this order, to go from raw sequenced exome reads to annotated tabular variant reports.
Galaxy Workflow files are JSON-formatted. You can edit them manually, or import
them into Galaxy and use Galaxy's graphical workflow editor, then download the
edited version again. Either way, you should pretty-format the edited file
before committing them to obtain nice and readable diffs.
Use Python's built-in json.tool command for this task:
python3 -m json.tool your_edited_workflow.ga > workflow_to_commit.ga
Python3.5 or later is required because earlier versions won't preserve element order.
When you edit a subworkflow, please note that the changes you make do not get reflected in the containing workflow (which carries its own embedded copy of the subworkflow). To make your changes visible in the containing workflow, you need to remove the embedded subworkflow from it and add the edited version back in.