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carpentries-incubator / workflows-snakemake

One-day Snakemake workshop.
https://carpentries-incubator.github.io/workflows-snakemake/
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collections to collections.abc and rulegraph #85

Open tijsbliek opened 3 years ago

tijsbliek commented 3 years ago

Hi,

Great lesson you have created here. That it even includes stuff like how to Run Snakemake on cluster computers makes it all very complete.

One warning I got is that the line ' from collections import Sequence ' in the plotcount.py will need to be updated to 'from collections.abc import Sequence' to avoid running into errors in upcoming versions of python.

Also it might be nice to add a rulegraph example in the lesson Final Notes, where also the DAG is mentioned. A DAG graph can get a bit unclear when making use of a lot of input files. The rulegraph makes a flow chard only including the rules and can give a more simplified picture of the pipeline. This can be implemented using something like the following line: ' snakemake --rulegraph | dot -Tsvg > rulegraph.svg '

Thanks for sharing this lesson.

cheers, tijs

tirkarthi commented 3 years ago

collections related warning was fixed upstream in https://github.com/hpc-carpentry/hpc-python/pull/31