This PR adds a new script to the docs make file that generates rulegraphs for our pipelines.
The script uses snakemake --rulegraph togheter with graphviz to create svg files that get written to the _static folder so they can be used in the docs.
Testing
Clone the repo and cd into the docs run the make command and check that the svg files are created. (note that some of the pipelines fails to generate graphs now without adding tweaking.)
make generate-doc-graphs
$ make generate-doc-graphs
bash generate-doc-graphs.sh
Generating rule graph: /Users/b260-admin/code/dkfz/deeprvat/docs/_static/preprocess_with_qc_rulegraph.svg
Building DAG of jobs...
Ok graph exists :)
---------
Generating rule graph: /Users/b260-admin/code/dkfz/deeprvat/docs/_static/preprocess_no_qc_rulegraph.svg
Building DAG of jobs...
Ok graph exists :)
---------
Generating rule graph: /Users/b260-admin/code/dkfz/deeprvat/docs/_static/annotations_rulegraph.svg
Building DAG of jobs...
Ok graph exists :)
---------
Generating dag graph: /Users/b260-admin/code/dkfz/deeprvat/docs/_static/annotations_dag.svg
Building DAG of jobs...
Ok graph exists :)
...
DONE!
What
This PR adds a new script to the docs make file that generates rulegraphs for our pipelines. The script uses
snakemake --rulegraphtogheter with graphviz to create svg files that get written to the _static folder so they can be used in the docs.Testing
Clone the repo and cd into the docs run the make command and check that the svg files are created. (note that some of the pipelines fails to generate graphs now without adding tweaking.)
make generate-doc-graphs