{"repo":"timtroendle/cookiecutter-reproducible-research","free":true,"listed":false,"github":"https://github.com/timtroendle/cookiecutter-reproducible-research","clone":"git clone https://github.com/timtroendle/cookiecutter-reproducible-research.git","description":"A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.","language":"CSS","stars":37,"topics":["cookiecutter-template","python","pandoc","automation","reproducible-research","snakemake","cluster-computing"],"license":"MIT","category":"workflow-automation","readme_excerpt":"cookiecutter-reproducible-research This repository provides cookiecutter templates for reproducible research projects. The templates do not attempt to be generic, but have a clear and opinionated focus. Projects build with these templates aim at full automation, and use Python 3.12 , conda , Git , Snakemake , and pandoc to create a HTML and PDF report out of raw data, code, and Markdown text. Fork, clone, or download this repository on GitHub if you want to change any of these. The template includes a few lines of code as a demo to allow you to create a report out of made-up simulation results right away. Read the README.md in the generated repository to see how. These templates are developed on macOS and tested on Linux. They may work with Windows Subsystem for Linux, but Windows is not actively supported. Template types default This generates the basic structure of a reproducible workflow. cluster The cluster template extends the basic template by adding infrastructure to support running on a compute cluster. Getting Started Make sure you have cookiecutter installed, otherwise install it with conda: conda install cookiecutter -c conda-forge Then create a repository using: cookiecutter gh:timtroendle/cookiecutter-reproducible-research --directory=[default/cluster] You will be asked for the following parameters: Parameter Description --- --- project name The name of your project, used in the documentation and report. project short name An abbreviation, used for environments a","default_branch":null,"files":null,"tree":[],"storefront":"/r/timtroendle","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/timtroendle/cookiecutter-reproducible-research/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}