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https://carpentries-incubator.github.io/workflows-snakemake/

One-day Snakemake workshop.
https://carpentries-incubator.github.io/workflows-snakemake/

alpha carpentries-incubator english lesson snakemake workflow-management

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One-day Snakemake workshop.

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README 

        
# Tame Your Workflow with Snakemake

This lesson teaches the basics of modern workflow engines

through [Snakemake](https://snakemake.readthedocs.io/en/stable/).



The example workflow performs a frequency analysis of several public domain

books sourced from [Project Gutenberg](https://www.gutenberg.org/), testing

how closely each book conforms to [Zipf's

Law](https://en.wikipedia.org/wiki/Zipf%27s_law). All code and data are

provided. This example has been chosen over a more complex scientific

workflow as the goal is to appeal to a wide audience and to focus on building

the workflow without distraction from the underlying processing.



At the end of this lesson, you will:



* Understand the benefits of workflow engines.

* Be able to create reproducible analysis pipelines with Snakemake.



## Topic breakdown



The lesson outline and rough breakdown of topics is in

[lesson-outline.md](_extras/lesson-outline.md).



## Lesson writing instructions



This is a fast overview of the Software Carpentry lesson template.



For a full guide to the lesson template, see the

[Software Carpentry example lesson](http://swcarpentry.github.io/lesson-example/).



### Lesson structure



Software Carpentry lessons are generally episodic, with one clear concept for each episode

([example](http://swcarpentry.github.io/r-novice-gapminder/)).



An episode is just a markdown file that lives under the `_episodes` folder.

Here is a link to a [markdown cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) with most markdown syntax.

Additionally, the Software Carpentry lesson template uses several extra bits of formatting - see here for a [full guide](http://swcarpentry.github.io/lesson-example/04-formatting/).

The most significant change is the addition of a YAML header that adds metadata (key questions, lesson teaching times, etc.)

and special syntax for code blocks, exercises, and the like.



Episode names should be prefixed with a number of their section plus the number of their episode within that section.

This is important because the Software Carpentry lesson template will auto-post our lessons in the order that they would sort in.

As long as your lesson sorts into the correct order,

it will appear in the correct order on the website.



### Publishing changes to Github + the Github pages website



The lesson website is viewable at [https://csiro-data-school.github.io/workflows/](https://csiro-data-school.github.io/workflows/).



The lesson website itself is auto-generated from the `gh-pages` branch of this repository.

Github pages will rebuild the website as soon as you push to the Github `gh-pages` branch.

Because of this `gh-pages` is considered the "master" branch.



### Previewing changes locally



Obviously having to push to Github every time you want to view your changes to the website isn't very convenient.

To preview the lesson locally, run `make serve`.

You can then view the website at `localhost:4000` in your browser.

Pages will be automatically regenerated every time you write to them.



Note that the autogenerated website lives under the `_site` directory

(and doesn't get pushed to Github).



This process requires Ruby, Make, and Jekyll. You can find setup instructions [here](http://swcarpentry.github.io/lesson-example/setup/).



## Example lessons



A couple links to example SWC workshop lessons for reference:



* [Example Bash lesson](https://github.com/swcarpentry/shell-novice)

* [Example Python lesson](https://github.com/swcarpentry/python-novice-inflammation)

* [Example R lesson](https://github.com/swcarpentry/r-novice-gapminder) (uses R markdown files instead of markdown)