- Set cancer_type and date_data to download Firehose data or provide own input file.
- Provide the remainder files related to the tumor type of the input file.
6. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet):
6. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet). Make sure the paths in the shell script are configured correctly.:
