snakemake-github-action
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snakemake
A Github action for running a Snakemake workflow
How do I specify the path to my config file? I've tried moving it around but the GH action doesn't seem to pick it up from anywhere automatically. .github/workflows/main.yaml ```...
I have a couple of error check rules to ensure a correct conig setup. I give those rules a higher priority so that they run first and it fails fast....
I had a problem in my snakemake workflow that was "hidden" by the fact that the tests run on github happily succeeded when they should have hung. When I ran...
Hi there, I am trying to create CI for a Snakemake workflow that needs to install several conda envs for different rules. Is there a way to use the GitHub...
I'm trying to make a GitHub action before and after a flow so that I can do a diff of the list-untracked before and after a flow runs so that...
I usually run this to make save DAGs ```bash snakemake --dag --forceall --configfile config/example.yml | dot -Tpng > outdir/full-graph.png ``` So I tried this ```yml - name: Save full DAG...
I keep getting an error message that says, "`Error: Snakefile "Snakefile" not found.`" My Snakefile is in `workflow/` and I have an `environment.yml` file in `workflow/envs/`. `workflow/` is in the...
Hi, is it possible to update the conda environment used in the github action? I think the current action uses `peppy=0.34.0`. I would like to update it to `0.35.1`
It would be really useful if one could set which snakemake version that should be used. Our workflows started to fail when a new version of snakemake was released.
When using the unit tests generated by Snakemake, I am unable to actually RUN the tests as the testing system does not re-set the default working directory to the project...
