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sars_cov_2 specific xref configuration

Marek Szuba requested to merge feature/sars_cov_2_conf into master

Created by: magaliruffier


  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing


Using one or more sentences, describe in detail the proposed changes. These configuration changes allow us to run the xref pipeline on the annotation for sars-cov-2

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. this is a virus genome with different data sources to the usual vertebrate species the added configuration ensure we use the correct data for the virus annotation without affecting existing settings for vertebrate species


If applicable, describe the advantages the changes will have. no changes required to existing pipeline to run on new virus genome

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.


Have you added/modified unit tests to test the changes? a full run of the pipeline was done with the changes

If so, do the tests pass/fail?

Have you run the entire test suite and no regression was detected? the data was reviewed manually and released as part of the COVID-19 browser

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