File Structure

(▶) Running & configuring pipeline (for User)

(🛠) Extending pipeline functions (for Developers)

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├── ci_lib (🛠)    | custom python package containing all custom functions for the pipeline steps
├── workflow (🛠)  | Snakemake logic like rules, envs and entry scripts
├── config (▶)    | config files for pipeline runs
├── resources (▶) | experimental data and brain atlases
├── results (▶)   | processed data and plots
└── SLURM     | batch files to run on computational clusters