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.

Category	Subworkflows	Workflows
alignment	minimap2, bwa-mem2, star, ultra, blastp, diamond-blastp
antigen prediction	mhcflurry2, netmhcpan4
assembly	hifiasm, rnabloom2, stringtie2
haplotyping	whatshap
hla typing	arcashla, hlaprofiler, seq2hla	short-read
isoform characterization	espresso, flair, isoquant, isoseq, isotools, mandalorion, rmats, sqanti3, talon	long-read, short-read
peptide prediction	mopepgen
quantification	bambu, kallisto, liqa, oarfish, salmon, transigner	long-read, short-read
read error correction	ratatosk
sequencing simulation	art, nanosim, neat, pbsim3
utilities	fastqc, pbccs, fastq2bam, coverage
variant annotation	vep
variant calling	47 tools including mutect2, deepvariant, delly2, sniffles2, manta, strelka2, and more	lr-germline, lr-somatic, sr-germline, sr-somatic
variant phasing	hiphase, whatshap

Dependencies

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

License

Licensed under the Apache License, Version 2.0.