Tutorial: Snakemake → DAGMan¶

In this tutorial we’ll convert a simple Snakemake workflow to HTCondor DAGMan, build its environments and validate the result.

Prerequisites¶

Docker daemon running (for image builds)
HTCondor client tools (optional – for submitting)

1. Clone the example workflow¶

git clone https://github.com/csmcal/wf2wf-examples.git
cd wf2wf-examples/snake/basic

2. Inspect the workflow¶

snakemake --dag --snakefile linear.smk | dot -Tpng > dag.png && open dag.png

3. Dry-run wf2wf¶

wf2wf info linear.smk

4. Convert with auto-env¶

wf2wf convert -i linear.smk -o linear.dag \
              --out-format dagman \
              --auto-env build \
              --push-registry ghcr.io/$USER/wf2wf-demo \
              --report-md

Outputs:

linear.dag – DAGMan workflow
linear.dag.md – conversion report
*.sub files – HTCondor submit descriptions
Images pushed with digest-tags

5. Validate¶

wf2wf validate linear.dag
wf2wf validate linear.dag.loss.json

6. Submit (optional)¶

condor_submit_dag -f linear.dag

That’s it! You can re-import the DAG back to Snakemake later.