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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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Note that the re-run triggers changed in Snakemake 7.8.0 #40

Closed jdblischak closed 1 year ago

jdblischak commented 1 year ago
Instructions Thanks for contributing! :heart: If this contribution is for instructor training, please email the link to this contribution to checkout@carpentries.org so we can record your progress. You've completed your contribution step for instructor checkout by submitting this contribution! Keep in mind that **lesson maintainers are volunteers** and it may take them some time to respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum. If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact The Carpentries Team at team@carpentries.org. You may delete these instructions from your comment. \- The Carpentries

Related to my review at https://github.com/carpentries-lab/reviews/issues/17

tbooth commented 1 year ago

This is part of the general issue of how to deal with Snakemake changes. Having dug down into the Snakemake code, I can say that the newer rerun triggers do not (at least a few months ago did not) actually work as advertised, and as Ezra noted in #36 there is some feeling in the community that detecting this set of changes is over-complex and problematic.

So I'll accept this PR for now but really I need to see if the course should be running with Snakemake 7 and if so what else in the course needs to change - probably not much structurally but a bunch of little details and sample outputs.