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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Trigger WDL tests on changes to /inputs and fix Terra config tests #691

Closed mwalker174 closed 3 months ago

mwalker174 commented 3 months ago

Another PR testing is failing with this error:

RUNNING TERRA INPUT VALIDATION NOW
Traceback (most recent call last):
  File "./scripts/test/terra_validation.py", line 135, in <module>
    main()
  File "./scripts/test/terra_validation.py", line 131, in main
    validate_all_terra_jsons(base_dir, womtool_jar, expected_num_inputs)
  File "./scripts/test/terra_validation.py", line 92, in validate_all_terra_jsons
    for wdl, json_file in get_wdl_json_pairs(os.path.join(base_dir, WDLS_PATH),
  File "./scripts/test/terra_validation.py", line 51, in get_wdl_json_pairs
    jsons = list_jsons(terra_inputs_paths, expected_num_inputs)
  File "./scripts/test/terra_validation.py", line 45, in list_jsons
    raise Exception(f"Expected {expected_num_jsons} Terra input JSONs but found {num_input_jsons}. To proceed anyway, edit the expected number of JSONs with the -n input.")
Exception: Expected 30 Terra input JSONs but found 21. To proceed anyway, edit the expected number of JSONs with the -n input.

This is seems to be the result of removing the single-batch workflow Terra configurations.

This PR fixes the error and also adds push/PR paths to include inputs/** changes for WDL testing on Github.

Edit: Also added dependent testing scripts to the trigger paths.