{"id":13478642,"url":"https://github.com/hpc-carpentry/old-hpc-workflows","last_synced_at":"2025-03-27T08:30:50.044Z","repository":{"id":47462498,"uuid":"504166561","full_name":"hpc-carpentry/old-hpc-workflows","owner":"hpc-carpentry","description":"Scaling studies on high-performance clusters using Snakemake workflows","archived":true,"fork":false,"pushed_at":"2023-03-10T19:20:41.000Z","size":10323,"stargazers_count":8,"open_issues_count":20,"forks_count":2,"subscribers_count":12,"default_branch":"gh-pages","last_synced_at":"2024-10-30T12:47:05.520Z","etag":null,"topics":["alpha","carpentries-incubator","english","hpc-carpentry","parallel-computing","snakemake-workflows"],"latest_commit_sha":null,"homepage":"https://www.hpc-carpentry.org/old-hpc-workflows/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/hpc-carpentry.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS"}},"created_at":"2022-06-16T13:28:03.000Z","updated_at":"2024-08-14T17:25:26.000Z","dependencies_parsed_at":"2024-01-16T07:22:19.455Z","dependency_job_id":"b9b11df6-c646-46fc-bc2b-d17cdd5300ce","html_url":"https://github.com/hpc-carpentry/old-hpc-workflows","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hpc-carpentry%2Fold-hpc-workflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hpc-carpentry%2Fold-hpc-workflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hpc-carpentry%2Fold-hpc-workflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hpc-carpentry%2Fold-hpc-workflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hpc-carpentry","download_url":"https://codeload.github.com/hpc-carpentry/old-hpc-workflows/tar.gz/refs/heads/gh-pages","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245809646,"owners_count":20676026,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alpha","carpentries-incubator","english","hpc-carpentry","parallel-computing","snakemake-workflows"],"created_at":"2024-07-31T16:01:59.775Z","updated_at":"2025-03-27T08:30:48.881Z","avatar_url":"https://github.com/hpc-carpentry.png","language":"Python","funding_links":[],"categories":["Python"],"sub_categories":[],"readme":"# Tame Your Workflow with Snakemake\nThis lesson teaches the basics of modern workflow engines\nthrough [Snakemake](https://snakemake.readthedocs.io/en/stable/).\n\nThe example workflow performs a frequency analysis of several public domain\nbooks sourced from [Project Gutenberg](https://www.gutenberg.org/), testing\nhow closely each book conforms to [Zipf's\nLaw](https://en.wikipedia.org/wiki/Zipf%27s_law). All code and data are\nprovided. This example has been chosen over a more complex scientific\nworkflow as the goal is to appeal to a wide audience and to focus on building\nthe workflow without distraction from the underlying processing.\n\nAt the end of this lesson, you will:\n\n* Understand the benefits of workflow engines.\n* Be able to create reproducible analysis pipelines with Snakemake.\n\n## Topic breakdown\n\nThe lesson outline and rough breakdown of topics is in\n[lesson-outline.md](_extras/lesson-outline.md).\n\n## Lesson writing instructions\n\nThis is a fast overview of the Software Carpentry lesson template.\n\nFor a full guide to the lesson template, see the\n[Software Carpentry example lesson](http://swcarpentry.github.io/lesson-example/).\n\n### Lesson structure\n\nSoftware Carpentry lessons are generally episodic, with one clear concept for each episode\n([example](http://swcarpentry.github.io/r-novice-gapminder/)).\n\nAn episode is just a markdown file that lives under the `_episodes` folder.\nHere is a link to a [markdown cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) with most markdown syntax.\nAdditionally, 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/).\nThe most significant change is the addition of a YAML header that adds metadata (key questions, lesson teaching times, etc.)\nand special syntax for code blocks, exercises, and the like.\n\nEpisode names should be prefixed with a number of their section plus the number of their episode within that section.\nThis is important because the Software Carpentry lesson template will auto-post our lessons in the order that they would sort in.\nAs long as your lesson sorts into the correct order,\nit will appear in the correct order on the website.\n\n### Publishing changes to Github + the Github pages website\n\nThe lesson website is viewable at [https://carpentries-incubator.github.io/hpc-workflows/](https://carpentries-incubator.github.io/hpc-workflows/).\n\nThe lesson website itself is auto-generated from the `gh-pages` branch of this repository.\nGithub pages will rebuild the website as soon as you push to the Github `gh-pages` branch.\nBecause of this `gh-pages` is considered the \"main\" branch.\n\n### Previewing changes locally\n\nObviously having to push to Github every time you want to view your changes to the website isn't very convenient.\nTo preview the lesson locally, run `make serve`.\nYou can then view the website at `localhost:4000` in your browser.\nPages will be automatically regenerated every time you write to them.\n\nNote that the autogenerated website lives under the `_site` directory\n(and doesn't get pushed to Github).\n\nThis process requires Ruby, Make, and Jekyll. You can find setup instructions [here](http://swcarpentry.github.io/lesson-example/setup/).\n\n## Example lessons\n\nA couple links to example SWC workshop lessons for reference:\n\n* [Example Bash lesson](https://github.com/swcarpentry/shell-novice)\n* [Example Python lesson](https://github.com/swcarpentry/python-novice-inflammation)\n* [Example R lesson](https://github.com/swcarpentry/r-novice-gapminder) (uses R markdown files instead of markdown)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhpc-carpentry%2Fold-hpc-workflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhpc-carpentry%2Fold-hpc-workflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhpc-carpentry%2Fold-hpc-workflows/lists"}