A custom cookiecutter template for my bioinfo projects
cookiecutter...obviously. Installation instructions here
To generate a new project, simply run
cookiecutter https://github.com/LisaHagenau/cookiecutter-template
This is the folder structure generated by the template:
./{{cookiecutter.directory_name}}/
|-- AUTHORS.md <- names of people working on the project
|-- README.md <- this file, explains what goes where and additional, project-specific information, e.g.prerequisites and how-to-use
|-- config <- configuration files for software, if needed
|-- data
| |-- external <- not your own data
| |-- interim <- intermediate data produced by analysis, can safely be deleted
| |-- metadata <- description of raw files goes here
| |-- processed <- final data used for the analysis, e.g. bam or variant files
| |-- raw <- raw data, read-only!
|-- docs <- everything that doesn't belong in references or reports
|-- enviroment.yml <- conda environment file
|-- logs <- log output from software goes here, create new subdirectories if needed
|-- references <- software manuals, literature
|-- reports <- annotated results in article or pdf form (e.g. R Notebooks or Markdown documents)
| |-- figures <- extra directory for figures
|-- src <- project source code: bash, python or R scripts