Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add AMR class and subclass tabular comparison tables. #31

Merged
merged 15 commits into from
Jan 10, 2024
Merged

Add AMR class and subclass tabular comparison tables. #31

merged 15 commits into from
Jan 10, 2024

Commits on Jan 10, 2024

  1. Fix nextflow config by including baseDir in the PYTHONPATH. 

    This is necessary to allow importing the zdb module containing
notably the database.
    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    450229d View commit details
    Browse the repository at this point in the history

  2. Add a test for amr hit extraction in annotation pipeline. 

    We also add the amr hits to the full pipeline test to allow us
to test the AMR views in the webapp tests.
    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    b56e405 View commit details
    Browse the repository at this point in the history

  3. Add tests for tabular comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    f39f248 View commit details
    Browse the repository at this point in the history

  4. Include hint to run tests with local metagenlab_libs in README.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    de7d654 View commit details
    Browse the repository at this point in the history

  5. Cleanup: remove forgotten print statement.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    0ee32be View commit details
    Browse the repository at this point in the history

  6. Refactor AmrComparisonView to make it reusable. 

    We will reuse this view to compare AMRs grouped by class and
subclass.
    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    858236d View commit details
    Browse the repository at this point in the history

  7. Add AMR class and subclass comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    18ce7f0 View commit details
    Browse the repository at this point in the history

  8. Link gene to NCBI in AMR comparison table.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    1e95270 View commit details
    Browse the repository at this point in the history

  9. Change amr_comparison path to amr_gene_comparison.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    870b058 View commit details
    Browse the repository at this point in the history

  10. Add test for new AMR comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    e7225ff View commit details
    Browse the repository at this point in the history

  11. Customize table help message for the different AMR comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    8f57982 View commit details
    Browse the repository at this point in the history

  12. Add tests that navigation is present in all tabular comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    fb7bab4 View commit details
    Browse the repository at this point in the history

  13. Add navigation tab to AMR comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    4809a15 View commit details
    Browse the repository at this point in the history

  14. Fix navigation for pfam and cog tabular comparison views.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    6c626bc View commit details
    Browse the repository at this point in the history

  15. Update changelog.

    @njohner
    njohner committed Jan 10, 2024
    Configuration menu
    Copy the full SHA
    07a7b4a View commit details
    Browse the repository at this point in the history