As mentioned earlier two snakemake workflows are available. One that prepares the annotation files (e.g. generation of index files etc) and one that processes the Ribo-Seq data.
#### Prepare annotation workflow
First of all go to the 'snakemake/prepare_annotation' directory and fill in the 'config.yaml' file. To make sure that everything is configured properly create a dag of the workflow.
```
bash create_snakemake_flowchart.sh
```
And finally run the pipeline. This script is configured for the Slurm Workload Manager
```
nohup bash run_snakefile.sh &
```
#### Process data workflow
Once the prepare_annotation pipeline is complete you can move to the 'snakemake/process_data' directory. Copy or create a hard link of the Ribo-Seq samples you want to process in the 'samples' directory. Fill in the config.yaml file.
Create the dag
```
bash create_snakemake_flowchart.sh
```
And finally run the pipeline. This script is configured for the Slurm Workload Manager