Nexus

NEXtflow’s Ultimate Streamliner

A command-line interface for running bioinformatics workflows written in Nextflow.

TipThree commands. That’s it.

nexus avail                                           # see what's available
nexus run --nf-workflow <WORKFLOW.nf> --help          # see the parameters
nexus run --nf-workflow <WORKFLOW.nf> [parameters]    # run it

Quick Start

1. Install

conda create -n nexus python=3.10
conda activate nexus
conda install bioconda::nextflow==24.10.0
pip install nexus-<version>.tar.gz --verbose

Download the latest release from GitHub Releases.

2. Pick a Workflow

nexus avail

3. Run

Subworkflow (single tool)

nexus run --nf-workflow variant_calling_mutect2.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --reference_genome_fasta_file hg38.fa \
    --output_dir results/

Workflow (multiple tools)

nexus run --nf-workflow variant_calling_short-read-dna-somatic.nf \
    -params-file params.yaml

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

How Nexus is Organized

Tools

Individual process definitions that wrap a single bioinformatics tool (e.g., samtools, gatk4, minimap2).

Subworkflows

Single-tool workflows that compose one or more tool processes into a complete analysis step (e.g., variant_calling_mutect2).

Workflows

Meta-workflows that orchestrate multiple subworkflows into end-to-end pipelines (e.g., variant_calling_short-read-dna-somatic).

What’s Available

Check out the Subworkflows and Workflows pages for the specific details.

Dependencies

• python (>=3.10)
• nextflow (>=24.10.0)
• pyyaml

License

Licensed under the Apache License, Version 2.0.