CDC User Guide

Environment Setup

1. Clone the repository to your local machine:

git clone https://github.com/CDCgov/tostadas.git
cd tostadas

2. Load the Nextflow module:

Initialize the nextflow module by running the following command:

ml nextflow

3. Ensure that Nextflow is available by running nextflow -v

Expected Output:

nextflow version <CURRENT VERSION>

4. Update the default submissions config file with your NCBI username and password, and run one of the following nextflow commands to execute the scripts with default parameters and the local run environment:

# update this config file (you don't have to use vim)
vim bin/config_files/default_config.yaml
# for virus reads
nextflow run main.nf -profile test,<singularity/docker/conda> --virus

The outputs of the pipeline will appear in the test_output folder within the project directory. You can specify an output directory in the config file or by supplying a path to the --output_dir flag in your nextflow run command.