Installation

September 20, 2025 · View on GitHub

Table of Contents

Environment Setup

Dependencies:

  • Nextflow v. 21.10.3 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 already have Nextflow installed in your local environment, skip ahead to step 5.

(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.

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) Install Nextflow using mamba and the bioconda Channel

mamba install -c bioconda nextflow

Run a test submission

(1) Update the default submissions config file with your NCBI username and password

# update this config file (you don't have to use vim)

vim conf/submission_config.yaml

(2) Run the workflow with default parameters and the local run environment

# test command for virus reads

nextflow run main.nf -profile mpox,test,<singularity|docker|conda> --workflow biosample_and_sra

The pipeline outputs appear in tostadas/results

Start submitting your own data

Create an NCBI Center Account. See NCBI Center Account

Choose a workflow and specify your profile or (optionally, for annotation and GenBank submission) an organism_Type and virus_subtype. See: Putting together the Nextflow command

Please read the Submission Guide for important details about parameters you need to specify. Please especially note the following: