Task Model¶

Tasks are async Flyte v2 functions that perform a single bioinformatics operation. Each task receives typed Asset inputs, fetches them to disk, runs a tool, and produces new assets.

Pattern¶

@tool_env.task
async def my_task(ref: Reference, aln: Alignment) -> Variants:
    await asyncio.gather(ref.fetch(), aln.fetch())
    # ... run tool using ref.path, aln.path ...
    vcf = Variants()
    await vcf.update(output_path, sample_id="NA12878")
    return vcf

Conventions¶

• One task per function, one function per operation
• Task files live in src/stargazer/tasks/, named by tool or domain
• Async is preferred for I/O operations
• Resource requests (CPU, memory, GPU) are specified via TaskEnvironment

Available Tasks¶

See the Catalog for a complete list of registered tasks.