nf-modules

NextFlow bioinformatics module management tool

Overview

nf-modules is a command-line tool for managing NextFlow bioinformatics modules. It provides simple commands to list available modules and fetch them for use in your NextFlow workflows. Many of these modules are modifications from nf-core. For official nf-core modules, please use https://github.com/nf-core.

Installation

PyPI

pip install nf-modules

Usage

Recommended minimal NextFlow project directory structure:

├── nextflow.config
├── main.nf
├── modules/
│   ├── local/nf-modules/ # Your custom modules (e.g., assembly.nf) and nf-modules (e.g., pyhmmsearch)
│   └── nf-core/ # Official nf-core modules
├── bin/
├── .gitignore
└── README.md

List available modules

# List all modules (names only)
nf-modules list

# Export as YAML format
nf-modules list -f yaml

# Filter modules by name
nf-modules list --filter spades

Fetch modules

# Fetch modules to default directory (modules/local/nf-modules/)
nf-modules fetch pyrodigal spades

# Fetch to custom directory
nf-modules fetch -o modules/local/nf-modules/ pyrodigal spades

# Fetch from specific git tag/branch
nf-modules fetch -t v0.1.0 pyrodigal spades # Version
nf-modules fetch -t dev -f pyrodigal spades # Branch (overwrite previous version with -f/--force)

Commands

list

List all available modules in the repository.

Options:

• -f, --format {list-name,list-version,yaml}: Output format (default: list-name)
• -t, --tag TAG: Git tag or branch to fetch from (default: main)
• --filter FILTER: Filter modules by name pattern (case-insensitive substring match)

Output Formats:

• list-name

  barrnap
  flye
  pyrodigal
  spades
  trnascanse
  ...
  

• yaml

  name: nf-modules
  dependencies:
  - barrnap=0.9--hdfd78af_4[2025.9.1]
  - flye=2.9.5--d577924c8416ccd8[2025.9.1]
  - pyrodigal=3.6.3.post1--py310h1fe012e_1[2025.9.1]

fetch

Download modules from the repository to a local directory.

Options:

• -o, --output-directory DIR: Output directory (default: modules/local/nf-modules/)
• -t, --tag TAG: Git tag or branch to fetch from (default: main)
• modules: One or more module names to fetch

Examples:

nf-modules fetch pyrodigal
nf-modules fetch pyrodigal spades flye
nf-modules fetch -o modules/local/nf-modules/ -t v1.0.0 pyrodigal spades

Utilities

compile-reads-table

Illumina

compile-reads-table -f Fastq/ -n "[ID]_R[DIRECTION]_001.fastq.gz" -x fastq.gz

Oxford Nanopore / PacBio

compile-reads-table -f Fastq/ -n "[ID].merged.fastq" -x fastq -L

Requirements

• Python 3.6+
• PyYAML
• Pandas ≥ 2.1.0

Repository

The modules are sourced from: https://github.com/jolespin/nf-modules

License

Apache 2.0