populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
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RecursionError when submitting cpg_workflows pipeline runs #775

Open vivbak opened 1 month ago

vivbak commented 1 month ago

Failing batch link: https://batch.hail.populationgenomics.org.au/batches/454658/jobs/1

Can be repro'd with the following launch.json

{
    "name": "SEQR loader",
    "type": "debugpy",
    "request": "launch",
    "program": "${workspaceFolder}/main.py",
    "justMyCode": false,
    "args": [
        "seqr_loader"
    ],
    "python": "path_to_python",
    "console": "integratedTerminal",
    "env": {
        "SM_ENVIRONMENT": "",
        "CPG_CONFIG_PATH": "gs://path_to_config_from_failed_batch",
        "PYTHONPATH": "${workspaceFolder}/seqr-loading-pipelines"
    }
}

Seems to be a pickling issue, though the latest attempt at resolving has not resolved the issue https://github.com/populationgenomics/production-pipelines/pull/772

First reported by @EddieLF