NextFlow bioinformatics modules management tool

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.

PyPI

pip install nf-modules

Recommended minimal NextFlow project directory structure:

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

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

# Fetch to custom directory
nf-modules fetch -o modules/external 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)

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]

Download modules from the repository to a local directory.

Options:

• -o, --output-directory DIR: Output directory (default: modules/external)
• -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/external -t v1.0.0 pyrodigal spades

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

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

• Python 3.6+
• PyYAML
• Pandas ≥ 2.1.0

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

Apache 2.0