To run full pipeline: i.e. Data preparation, cleaning, splitting, sequence encoding, training, testing and proof of concept
N E X T F L O W >= 22.04.0
nextflow run Rudolph-afk/Zoon0PredV -params-file params/params.yml
N E X T F L O W < 22.04.0
nextflow run Rudolph-afk/Zoon0PredV -params-file params/params.yml -dsl2
| Directory/File | Contents |
|---|---|
| app | Project dashboard app |
| assets | Figures and tables |
| bin | Scripts used in the pipeline |
| conf | Nextflow pipeline configuration files |
| data | Input data for the pipeline |
| image-defs | Singularity container definition files |
| modules | Nextflow process definitions |
| workflows | Nextflow workflow definitions |
| notebooks | ipynb notebooks for prototyping and project figure generation |
| run_scripts | Custom scripts to run the pipeline |
| params | Parameter files for the pipeline |
| main.nf | Main script |
| nextflow.config | Main Nextflow configuration file |
This project is part of a MSc thesis entitled A DEEP LEARNING APPROACH TO PREDICTING POTENTIAL VIRUS SPECIES CROSSOVER USING CONVOLUTIONAL NEURAL NETWORKS AND VIRAL PROTEIN SEQUENCE PATTERNS submittted to the University of the Western Cape.