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I have a long snakemake workflow processing 9 samples with many parallel rules. When I create a picture for the DAG with:
snakemake --forceall --dag | dot -Tpdf > dag.pdf
the resulting dag plot is huge and very redundant (and ugly because of complex node placement).
Is it possible to produce a canonical dag plot that will not show the 9 nodes for each task but only the main path through all steps?
I thought od simplifying my sample list to one sample but hope there is a better method without touching the snakefile (secret parameters?)
Thanks
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Summary: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition.
-R selects the one rule (and all its dependent rules also!), -n does a "dry run", it just prints what it would do without -n.
Snakefiles are Python code. Completing the Pipeline. Resources and parallelism. Make your workflow portable and reduce duplication. Scaling a pipeline across a cluster.
Use the flag --rulegraph instead of --dag.
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