chewBBACA Import

The Import page (admin only) lets you upload chewBBACA results_alleles.tsv files directly into MIMOSA. Imported samples are stored in the database and included in the next pipeline run.

  1. Navigate to Import in the dashboard sidebar.

  2. Drag-and-drop one or more .tsv files onto the upload area, or click to browse. Folders are supported.

  3. Select the Profile that matches the organism (e.g. staphylococcus aureus).

  4. If any sample IDs already exist in the database, a conflict table appears. Resolve each duplicate:

    • Skip — leave the existing record unchanged (default).

    • Replace — overwrite the existing allele data.

    • Rename — import under a new sample ID.

  5. Click Import N samples to submit.

Demo data

The repository ships with a small test dataset you can use to test MIMOSA:

  • test/MIMOSA_test_results_alleles.tsv — 15 Staphylococcus aureus allele profiles ready for drag-and-drop import.

  • test/MIMOSA_test_Metadata.xlsx — matching metadata (hospital, postcode, date) in Excel format, for drag-and-drop onto the Samples page.

  • test/MIMOSA_test_Metadata.csv — same metadata in CSV format, used with --supplementary_metadata in CLI runs.

UI import (drag-and-drop)

  1. Open the Import page and drag test/MIMOSA_test_results_alleles.tsv onto the upload area.

  2. Select staphylococcus_aureus as the profile and click Import 15 samples.

  3. The samples will appear in the Pending for next run table; use the Run pipeline button to cluster them.

  4. After clustering, drag test/MIMOSA_test_Metadata.xlsx onto the Samples page to apply hospital, postcode and date metadata.

Full pipeline including metadata (CLI)

python test/mimosa_chewbbaca_test.py --credentials credentials.json

This runs main.py with the test TSV, the supplementary metadata CSV, and --bonsai false. To clean up afterwards:

python test/mimosa_chewbbaca_test.py --credentials credentials.json --delete

Importing via the command line

chewBBACA files can also be passed directly to the pipeline using the --chewbbaca flag:

python scripts/main.py \
  --credentials credentials.json \
  --chewbbaca /data/results_alleles.tsv \
  --chewbbaca_profile staphylococcus_aureus

See Pipeline for the full reference including directory inputs, CSV manifests, and conflict behaviour.