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carpentries-incubator / snakemake-novice-bioinformatics

Introduction to Snakemake for Bioinformatics
https://carpentries-incubator.github.io/snakemake-novice-bioinformatics
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Solution to Ep07 does not work #66

Open tbooth opened 3 months ago

tbooth commented 3 months ago

From @cmeesters:

Chapter 7 - Finishing Again, a nice description. The solution, however, does not work,

and stating in the file # "rule all_counts" has been removed to reduce clutter might seem like a good idea, but a "solution" for reference should be well tested and complete up to the description in the chapter.

tbooth commented 3 months ago

I have now added .github/workflows/code-test-ubuntu.yml and directory of .test/ files which performs a CI test of all the sample solutions. This is not (yet?!) testing solutions embedded in the Markdown, but all files linked at the end of the episodes are auto-tested and confirmed working. Any regressions will be flagged under GitHub Actions. I'm not sure what problem was found with ep07, as the CI test passes without modification.

I disagree with the second comment. The all_counts rule is added at first to demonstrate simple aggregation but is later replaced with the MultiQC rule which performs the aggregation step, so there is no need to keep it in the later answers.