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Installation

Environment Setup

Dependencies:

  • Nextflow v. 21.01.03 or newer
  • Compute environment (docker, singularity or conda)

❗ Note: If you are a CDC user, please follow the set-up instructions found on this page: CDC User Guide

(1) Clone the repository to your local machine:

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

❗ Note: If you have mamba or nextflow installed in your local environment, you may skip steps 2, 3 (mamba installation) and 6 (nextflow installation) accordingly.

(2) Install mamba and add it to your PATH

2a. Install mamba

❗ Note: If you have mamba installed in your local environment, skip ahead to step 3 (Create and activate a conda environment)

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download Mambaforge-$(uname)-$(uname -m).sh bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge

2b. Add mamba to PATH:

export PATH="$HOME/mambaforge/bin:$PATH"

(3) Create and activate a conda environment

3a. Create an empty conda environment to install Nextflow into

conda create --name tostadas

3b. Activate the environment

conda activate tostadas

Verify which environment is active by running the following conda command: conda env list. The active environment will be denoted with an asterisk *

(4) Install Nextflow using mamba and the bioconda Channel

Install Nextflow

mamba install -c bioconda nextflow

Ensure installation was successful by running nextflow with the -v or -version flag

nextflow -v

Expected output:

nextflow version <CURRENT VERSION>

The exact version of Nextflow returned will differ from installation to installation. It is important that the command executes successfully, and a version number is returned.

(5) Update the default submissions config file with your NCBI username and password, and run the following nextflow command 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

❗ Note: If you do not update the default_config.yaml file with your NCBI credentials, you will see the following command error: Error:530 Login incorrect.

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.