sangeranalysis.engine/.vscode/launch.json

{
    // Use IntelliSense to learn about possible attributes.
    // Hover to view descriptions of existing attributes.
    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
    "version": "0.2.0",
    "configurations": [
        
        {
            "name": "Python Debugger: Current File with Arguments",
            "type": "debugpy",
            "request": "launch",
            "program": "${workspaceFolder}/src/nsbdiagnosistoolkit/cli/root.py",
            "console": "integratedTerminal",
            "args": [
                "-fa",
                "${workspaceFolder}/tests/resources/tohama_I_bpertussis.fasta",
                "-ipdbmlst",
                "pubmlst_bordetella_seqdef",
                "${workspaceFolder}/output"
            ],
            "cwd": "${workspaceFolder}/src",
            "env": {
                "PYTHONPATH": "${workspaceFolder}/src"
            }
        }
    ]
}