├── .github ├── CODEOWNERS └── workflows │ └── test_and_build.yml ├── .gitignore ├── AUTHORS ├── CITATION ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Gemfile ├── LICENSE.md ├── Makefile ├── README.md ├── _config.yml ├── _episodes ├── .gitkeep ├── 01-basics.md ├── 02-scripts.md ├── 03-lists.md ├── 04-dicts.md ├── 05-functions.md ├── 06-parallel.md ├── 07-snakemake-intro.md ├── 08-snakefiles.md ├── 09-wildcards.md ├── 10-patterns.md ├── 11-snakemake-python.md ├── 12-resources.md ├── 13-cluster.md └── 14-final-notes.md ├── _extras ├── .gitkeep ├── about.md ├── discuss.md ├── figures.md └── guide.md ├── _includes ├── all_figures.html ├── figure.html └── links.md ├── aio.md ├── bin ├── chunk-options.R ├── extract_figures.py ├── generate_md_episodes.R ├── knit_lessons.sh ├── lesson_check.py ├── lesson_initialize.py ├── markdown_ast.rb ├── repo_check.py ├── run-make-docker-serve.sh ├── test_lesson_check.py ├── util.py └── workshop_check.py ├── code └── .gitkeep ├── commands.mk ├── data └── .gitkeep ├── fig ├── .gitkeep ├── 02-challenge-dag.svg ├── 02-dats-dag.svg └── 05-final-dag.svg ├── files ├── .gitkeep ├── snakemake-lesson.tar.gz ├── snakemake-lesson.zip └── snakemake-lesson │ ├── .Snakefile │ ├── books │ ├── LICENSE_TEXTS.md │ ├── abyss.txt │ ├── isles.txt │ ├── last.txt │ └── sierra.txt │ ├── cluster.json │ ├── matplotlibrc │ ├── plotcount.py │ ├── wordcount.py │ └── zipf_test.py ├── index.md ├── lesson-outline.md ├── reference.md └── setup.md /.github/CODEOWNERS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hpc-carpentry/hpc-python/HEAD/.github/CODEOWNERS -------------------------------------------------------------------------------- /.github/workflows/test_and_build.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hpc-carpentry/hpc-python/HEAD/.github/workflows/test_and_build.yml 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