This workflow processes wastewater samples for the detection of drug resistance mutations.
Input:
- aligned samples (alignment with V-pipe)
- positions of interest: positions where drug resistance mutations are expected
- list of all samples to be processed
Output:
- csv file of all mutations at positions of interest --> This file can be used in the visualisation notebook to create a heatmap
To run this workflow adapt file paths in config and sample names. Run the pipeline on Euler with run_workflow.sh.
Note, at the moment the workflow is SARS-CoV-2 specific, however, reference files and gene annotations can be easily swapped.