Use xopen throughout the code

LUMC / pytest-workflow

Configure workflow/pipeline tests using yaml files.

https://pytest-workflow.readthedocs.io/en/stable/

GNU Affero General Public License v3.0

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Use xopen throughout the code #178

Open rhpvorderman opened 1 year ago

rhpvorderman commented 1 year ago

Since #177 xopen is now a dependency of pytest-workflow. This allows openng various compressed files without problems. Currently some parts of the code still manually checked whether a gzip handler is needed. This can now be replaced by xopen.