Analysing Cancer Data

This project aims to explore and analyse cancer data for educational purposes.

Download data

Install AWS CLI from: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html

Run the following command from the root directory of this project:

aws s3 cp s3://icgc25k-open/PCAWG/consensus_snv_indel/final_consensus_passonly.snv_mnv_indel.icgc.public.maf.gz data --endpoint-url https://object.genomeinformatics.org --no-sign-request

Install libraries

Install all requirements:

pip install -r requirements.txt

If you want to use GPU, run this after the pip install:

pip uninstall torch -y
conda install pytorch pytorch-cuda -c pytorch -c nvidia

Run the pipeline

To run the NextFlow pipeline:

nextflow run main.nf