gpas-tb-CI-testing

Automated end-to-end testing of the GPAS TB pipeline.

Even without generating samples on each run, this will likely take 4h+ to complete. Each pipeline will likely take 1-1.5h + downloading prerequisites (several GB)

Testing steps

1. Generate synthetic TB samples with known variations
2. Run these samples through lodestone to produce VCF files
3. Run these samples through gnomonicus to produce an antibiogram

Test cases

Currently there are a few test cases used. Most are derrived from clinical importance (such as XDR samples), but a few edge cases have been included from the WHO TB catalogue

• MDR - Resistant to RIF & INH (rpoB@S450L, katG@S315T)
• preXDR - MDR & fluoquinolone resistant (rpoB@S450L, gyrA@A90V, gyrA@S95T)
• XDR - preXDR & >=1 of AMI, KAN, CAP resistance (rpoB@S450L, gyrA@A90V, gyrA@S95T, rplC@C154R)
• WHO - A wide selection of mutations covering simple SNPs, indels, multi-mutations, revcomp indels, non-coding SNPs etc