When debugging a Snakemake workflow, it’s helpful to run the JIT step locally instead of re-registering your workflow every time you want to test a change. To address this, the Latch SDK supports local development for Snakemake workflows.
If you are unfamiliar with the
latch develop command, please read about Local Development before continuing.
Run the following command to use
latch develop with your Snakemake workflow:
$ latch develop . --snakemake
To run the JIT task, create a test file that calls the task function defined in
snakemake_jit_entrypoint.py with test inputs.
$ cat scripts/dry_run.py
from snakemake_jit_entrypoint import your_workflow_name_jit_register_task
You can execute the script in your
latch develop session like so:
$ python3 scripts/dry_run.py
Note: If you are running into an
ImportError, be sure to use the version of Python in which the Latch SDK was installed.