Add aws credentials before running the script as:
nextflow run main.nf [-resume] [-with-report report.html]
The Pipeline is split into three parts: align, variantCall and annotation. User can also choose to run exomiser following annotation
To run, go to individal folder and run nextflow run [pipeline name].nf
The flask folder has a script to lunch an API server to accept tasks either to run the complete set of the pipeline, or part of it.
To run, go to the flask folder and run python main.py (probably want to edit the config.yml in the same folder to adapt your working evironment).