Testing and Validation
Test Data Set
Both WGS and WES aligned BAM files were used to test in single and tumor-normal paired modes.
| Type | Mode | Size | CPU threads | PeakVMemory | Run Time | |
|---|---|---|---|---|---|---|
| 1 | WES | Single | 4GB | 72 | 9.381 GB | ~4 min |
| 2 | WES | Paired | 4GB/4GB | 72 | 12.317 GB | ~8 min |
| 3 | WGS | Single | 399GB | 72 | 21.042 GB | ~2h 40 min |
| 4 | WGS | Paired | 399GB/740GB | 72 | 26.615 GB | ~5 hours |
Running Tests with NFTest
Ensure NFTest is installed on your system. If it is not installed follow installation instructions in the NFTest documentation.
To test annotators run the command with the annotator of interest:
nftest run [test-paired-01 test-single-normal-01 test-single-tumor-01 test-paired-10 test-single-normal-10 test-single-tumor-10]
Additionally it is possible to modify the nftest.yml file to tune testing.
All testing assets can be found in the test/ directory.
For larger jobs a cluster submission tool is available for NFTest.
Validation Tool
Included is a template for validating your input files. For more information on the tool check out: https://github.com/uclahs-cds/tool-validate-nf