Initiate a project structure

init_project.sh

#!/usr/bin/env bash
# initiate a project directory structure
mkdir -p Backups             # to store any backup
mkdir -p Data/Raw_data       # raw data
mkdir -p Data/Raw_data/geno  # genotypes are in a sub-dir (add more if needed)
mkdir -p Data/Proc_data      # processed, i.e. cleaned data at different steps. Use horizontal dirs for middle steps.
mkdir -p Masters             # Main wrappers to run the pipeline (usually bash)
mkdir -p Programs/Scripts    # Collection of scripts (any language)
mkdir -p Programs/Scripts/R_func # Collection of R functions (which can be re-used from other projects)
mkdir -p Programs/Software   # Binaries and executables with their licences 
mkdir -p Programs/Parameters # Any specific parameter file, e.g. co-variance files.
mkdir -p Runs                # Different analyses/scenarios/model tested, consecutevly numbered as 001, 002 etc (keep a separate legend)
mkdir -p Outputs/Tables      # Ouput.csv tables
mkdir -p Outputs/Figures     # Plots and figures in general
mkdir -p Outputs/Reports     # Reports e.g. Rmarkdown
mkdir -p Logs                # Logs of analyses/scripts/masters etc.