snakemake / snakemake/snakemake

Include rules following a checkpoint in DAG visualization

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enhancement
Dominant language
Python
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Merged PRs (30d)
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Description

In workflows containing a checkpoint, the DAG cannot be completely visualized.

E.g. when running the second checkpoints example from the documentation, the DAG before workflow execution looks like so (collapsing all samples into one for simplicity):

clustering -> aggregate -> all

while after running the pipeline, the DAG looks like:

intermediate -> aggregate -> all

The desired outcome would be to have all steps displayed in one graph, like so:

clustering -> intermediate -> aggregate -> all

This may not be possible before workflow execution, but after workflow execution would be useful too.

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  3. Fork the repository and make your change on a branch.
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Research direction

Reproduce the second checkpoints example linked in the issue and compare the DAG before and after workflow execution. Trace the DAG visualization entry point responsible for those graphs; done means the post-execution visualization includes clustering, intermediate, aggregate, and all in one graph.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-engineering
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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