bactopia-test
Run nf-test suites for Bactopia components.
Discovers and executes nf-test files across modules, subworkflows, and workflows. Results are classified by status and displayed as a summary table. Per-test logs are saved to a logs/ directory.
Usage
bactopia-test [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--bactopia-path | STRING | Directory where the Bactopia repository is stored | |
--test-data | STRING | Directory containing bactopia-tests data (sets BACTOPIA_TESTS env). Required unless --cleanup |
Cleanup
| Option | Type | Default | Description |
|---|---|---|---|
--cleanup | BOOL | false | Find and remove all .nf-test/ temp files, then exit (no tests run) |
--dry-run | BOOL | false | With --cleanup, list what would be removed without deleting |
--keep | BOOL | false | Keep .nf-test/ directories and logs after tests pass (useful for debugging) |
Test Selection
| Option | Type | Default | Description |
|---|---|---|---|
--tier | CHOICE (modules, subworkflows, workflows, all) | all | Which component tier to test |
--include | STRING | Comma-separated list of component names to include | |
--exclude | STRING | Comma-separated list of component names to exclude |
Execution Options
| Option | Type | Default | Description |
|---|---|---|---|
--profile | CHOICE (docker, singularity, conda) | docker | Nextflow profile to use for tests |
--condadir | STRING | /home/rpetit3/.bactopia/conda | Directory where Conda environments are stored (NXF_CONDA_CACHEDIR env variable takes precedence) |
--singularity_cache | STRING | /home/rpetit3/.bactopia/singularity | Directory where Singularity images are stored (NXF_SINGULARITY_CACHEDIR env variable takes precedence) |
--generate | BOOL | false | Generate mode: delete snapshots and run twice to verify reproducibility |
--jobs | INT | 64 | Number of parallel test workers |
--fail-fast | BOOL | false | Stop on the first test failure instead of continuing |
--timeout | INT | 90 | Per-test timeout in minutes. Each nf-test subprocess is killed after this duration. Set to 0 to disable |
Output Options
| Option | Type | Default | Description |
|---|---|---|---|
--outdir | STRING | . | Directory to write the logs/ folder into |
--json | BOOL | false | Output results as JSON |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--verbose | BOOL | false | Print debug related text |
--silent | BOOL | false | Only critical errors will be printed |
--version, -V | BOOL | false | Show the version and exit. |