Change words/books example to genomic use case

[mgalland]

Hello hpc-carpentry team,

I am an Carpentry Instructor and I'd be quite interested to turn this lesson into an official Data Carpentry lesson ultimately as I see a considerable interest for Snakemake among Life Scientists.

As Snakemake is primarily used in genomics as far as I can tell, I'd like to change the example from words and books to some small sequencing dataset.
An example can be seen here in the official Snakemake read the docs.

What do you think?
Cheers
Marc

[psteinb]

Dear Marc, I think this is an excellent idea. I'd personally vote to first remove the python intro part from this repo in favor of 2 other excellent lessons on learning python [1] and [2], see #13 for details. Once this is approved, I am fine adding your example. However, I would strongly suggest not to make it the default example, but rather opt-in. The "books" example currently has a low entry barrier, which proved very suitable in the domains where I currently teach this lesson (image analysis, synchrotron physics and material simulation). I would disagree with your assertion that snakemake is used primarily in genomics. The latter is the cradle of snakemake, yes, but the tool lends itself to a far more general audience than this. How do you feel? [1]: https://github.com/swcarpentry/python-novice-inflammation [2]: https://github.com/swcarpentry/python-novice-gapminder

[mgalland]

Hello Peter,

Thank you for your feedback. Indeed, other SWC lessons do a great job to introduce Python and therefore the intro parts could probably be left out. If you are interested in Snakemake, that probably means that you are not a pure Python beginner anymore!

Indeed, Snakemake can be used for much more than genomics. Have you seen it used a lot for other things than genomics? I personally haven't but curious to see other use cases.

I agree that genomics should not be the default example. Too specific for sure. Would there be a way to "select" a domain of interest on the website (from a drop-down list for instance) so that some episodes with domain-specific would be updated?