snakemake-logger-plugin-biffix

A Snakemake (9.0 or later) logger plugin that reports a workflow's progress to biffix, the AWS-native control plane for running and tracking workflows. It is the Snakemake counterpart of the nf-biffix Nextflow plugin in ../nf-biffix, and both report the same wire contract (schemas/wire.engine.schema.json).

What it does

The plugin maps Snakemake's log records to biffix engine events (run_started, run_progress, run_dag, task_created, task_submitted, task_retrying, task_succeeded, task_failed, task_outputs and engine_task_verdict) and sends each one to two places:

• The ingest route, live. Events are buffered and POSTed in batches to {ingest_url}/events, bearer-authenticated with the run's capability token, by a background thread, so Snakemake's logging never waits on the network. Failed requests are retried or dropped; a lost POST never fails the workflow.
• A durable events.jsonl. Every event is also appended to a local file, which the biffix coordinator uploads and replays through ingest when the run exits, so an event the live POST dropped still arrives (ingest dedupes the repeats).

For a job on AWS Batch, the plugin emits task_submitted carrying the Batch job id, read from the payload the AWS Batch executor plugin attaches to its log records, and AWS EventBridge supplies the job's terminal state. For a local rule, which runs on the coordinator and never reaches Batch, the plugin emits the terminal event itself.

The plugin has no dependencies beyond snakemake-interface-logger-plugins; it uses only the standard library for HTTP.

How biffix uses it

biffix builds the plugin into a wheel for the coordinator base image (docker/coordinator/build-wheels.sh) and installs it into each Snakemake runtime layer (codebuild/runtime/build.sh). The coordinator (docker/coordinator/lib/snakemake.sh) runs Snakemake with --logger biffix and sets the variables below. The version in pyproject.toml must match logger_version in crates/biffix-workflow/src/runtime/pins.rs; a test in runtime/tests.rs checks it.

Configuration

Enable it with snakemake --logger biffix. Each setting comes from an environment variable or a command-line option; a non-empty option wins.

Snakemake's own derived variables (SNAKEMAKE_LOGGER_BIFFIX_*) are not read; the BIFFIX_* names are the only environment channel.

Development

uv sync --dev
uv run ruff check . && uv run ruff format --check .
uv run validate-pyproject pyproject.toml && uv run mypy
uv run pytest

The tests read files from the biffix repository's schemas/ directory, so they run from a biffix checkout: test_schema_conformance.py checks every emitted event against the engine wire schema, and test_ingest_limits.py checks that the poster's limits (largest batch, largest body, buffer size, retries and timeouts) equal schemas/ingest-limits.json, which biffix-core writes from the constants the ingest route enforces.

License

MIT; see LICENSE.

NOTICE

Parts of handler.py, remote_adapter.py and writer.py (Snakemake log record parsing, the remote executor payload adapter and the JSONL event writer) are adapted from the snakemake-logger-plugin-snakesee package of snakesee. This package does not depend on snakesee. snakesee is distributed under the following license:

MIT License

Copyright (c) 2024 Fulcrum Genomics LLC

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