ShawHahnLab / umbra

Python package and executable for Linux for managing Illumina sequencing runs
GNU Affero General Public License v3.0
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Metadata output not respecting configured output path for implicit tasks #44

Closed ressy closed 5 years ago

ressy commented 5 years ago

When the list of tasks does not explicitly include the word "metadata" the metadata task output should arrive in the directory specified by implicit_tasks_path. This worked before the reorganization in #41 and the always-explicit feature in #42.

ressy commented 5 years ago

Aha, the problem is the updated task setup in 698227d, specifically here. That shouldn't just assign the same list to a new name; then we end up modifying the original in-place (rookie mistake!) which takes effect across the main config and adds extra tasks to the "null" list.

Just slicing it for a shallow copy should be enough here since it's just a bunch of strings.

tasknames = self.config["task_null"][:]

No single unit test would easily catch this, but integration testing would.