garggroup / biodivgenomics Goto Github PK

This issue ticket is for a task note. Rename the current input parameter data_type ("HIFI"/"ONT") to seq_data_type. Because we want to add a new input parameter genome_data_type.

• seq_data_type: "HIFI" or "ONT"
• genome_data_type: ("organelle" or "mitochondria") or "" (empty). Note the mitochondria is a part of the organelle.

This is a note not to forget. The current test/test.py has 7 unit test cases (test_* methods). And the case test_all executes the WDL file by Dockstore CLI (run_wdl_by_dockstore_cli), and other test cases execute the directory by Cromwell cromwell-N.jar.

• Running by Docksotre CLI: Convenient to run locally. But possibly a bit slow to run on CI. A bit more user-friendly.
• Running by Cromwell directly. A lightweight. Perhaps the use case is a bit harder, as it creates the the cromwell-executions and cromwell-workflow-logs directories on the current working directory with root permission. This is good to run on the GitHub Actions CI environment.

The solution is to run test conditionally by Dockstore CLI or Cromwell Jar with an environment variable such as TEST_DOCKSTORE=true.