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Use default config.yaml instead of profiles to define .test as the working directory - #14
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Hey @dgruano, thanks for the effort here. I have cleaned the config files, stale code, documentation, and included an additional test for CI/CD to make sure we do not have this issue in the future. I have checked all the points in the I still have to fix a minor bug with differential expression (LRT running when there are less than 3 levels) and double check the docs, but we are almost ready for a new release. Great work, I really appreciate it! |
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What & why
In PR #7 we fixed the linting, but introduced another unexpected bug: since the working directory is defined in a profile at
profiles/default/config.yaml, it will always get loaded as a local profile (--worflow-profile) on top of the global profile (--profile). This will force execution under the.testdirectory even if the user defines a global profile with a differentdirectoryparameter, making it very conterintuitive and difficult to debug.After discussing with @Sergio-ote , we decided to stop using profiles for this and use the default workflow config to define all parameters relative to
.test. Since the user will always have to edit the default configuration to adapt the pipeline to their needs, this is not only the simplest but also the easiest for the user.Validation
.test/.test/dry-run builds the CoreBlock DAGworkflow/schemas/config.schema.yamlmkdocs build --strictpasses, if documentation was changed