Project template for setting up a directory and file structure for a new research project. The intended contents of each directory is explained in separate README.md files.
project
|- doc/ documentation for the study
|
|- data/ raw and primary data, essentially all input files, never edit!
| |- raw_external/
| |- raw_internal/
| |- meta/
|
|- code/ all code needed to go from input files to final results
|- notebooks/
|
|- intermediate/ output files from different analysis steps, can be deleted
|- scratch/ temporary files that can be safely deleted or lost
|- logs/ logs from the different analysis steps
|
|- results/ output from workflows and analyses
| |- figures/
| |- tables/
| |- reports/
|
|- .gitignore sets which parts of the repository that should be git tracked
|- Snakefile project workflow, carries out analysis contained in code/
|- config.yml configuration of the project workflow
|- environment.yml software dependencies list, used to create a project environment
|- Dockerfile recipe to create a project container