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Installation

TaxTriage requires two primary dependencies:

  1. Nextflow - the workflow engine
  2. Docker or Singularity - for containerized module execution

1. Install Nextflow

Follow instructions at nf-co.re/docs/usage/installation or run the following in a WSL2, native Linux, or macOS terminal:

# Verify Java 17+ is installed (required by Nextflow 24+)
java -version

# Download and install Nextflow
curl -fsSL get.nextflow.io | bash

Move the binary to your $PATH:

# Personal path (no sudo required)
mv nextflow ~/bin/

# System-wide (requires sudo)
sudo mv nextflow /usr/local/bin

Verify the installation:

nextflow -v

HPC users: Make sure nextflow is in your $PATH if it's not globally available on your cluster.

2. Install a Container Runtime

You only need one of the following. Docker is recommended for local workstations; Singularity is common on HPCs.

Follow the OS-specific instructions at docs.docker.com/engine/install.

Windows users (WSL2): Install Docker Desktop for Windows - it will be available automatically inside your WSL2 environment.

B. Singularity (HPC)

Follow the Singularity installation guide.

Important: Only SingularityCE v4+ is supported. Consult your HPC IT team if Singularity is not already available as a module.

When using Singularity, it is strongly recommended to pre-download containers before running the pipeline offline:

nf-core download https://github.com/jhuapl-bio/taxtriage --singularity-cache-only

Set the cache directory to avoid re-downloading images:

export NXF_SINGULARITY_CACHEDIR=/path/to/singularity/cache

3. Optional: Limit Nextflow JVM Memory

In some environments, the Nextflow Java Virtual Machine requests excessive memory. Add the following to your ~/.bashrc or ~/.bash_profile:

export NXF_OPTS='-Xms1g -Xmx4g'

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