GitHub - royjacobson/nf-python: Nextflow plugin enabling seamless integration between Nextflow and Python 🧪

3 min read Original article ↗

nf-python is a Nextflow plugin enabling seamless integration between Nextflow and Python scripts. Python scripts can be invoked as part of your Nextflow workflow, and arguments and outputs will be serialized back-and-forth automatically, making them available as native pythonic objects.

Installation

To use the plugin in your Nextflow data pipelines, simply include it by writing include { pyFunction } from 'plugin/nf-python' and it will be downloaded and installed. For all setup options, please refer to the Nextflow plugins documentation.

nf-python requires a working python installation in the execution environment. By default, the python in path will be used. It is also possible to specify a path to a specific python executable or a conda environment. Either in the configuration file:

nf_python {
  // Option 1
  executable = '/usr/bin/python'
  // Option 2
  conda_env = ''
}

The supported values for the conda_env option are the same ones supported by Nextflow's native conda support, and is using the same configuration options. Here are a few options:

  1. A list of required packages (e.g. conda_env = 'numpy biopython')
  2. A conda configuration file (e.g. conda_env = '/opt/task-env.yml')
  3. A path to an existing conda environment (e.g. conda_env = '/home/user/.conda/envs/my-env')

It is also possible to specify different environments on a per-function basis:

pyFunction(script: "", x: 1, y: 2, _executable: "/usr/bin/python")
pyFunction(script: "", x: 1, y: 2, _conda_env: "matplotlib")

Example Usage

To use a python script as part of your Nextflow pipeline, import pyFunction from the nf-python plugin:

include { pyFunction } from 'plugin/nf-python'

pyFunction('my_other_script.py', foo: 'too')

Usage inside python is easy:

  • Arguments (like foo) are passed as nf_python.nf.args.
  • To return results to nextflow, use nf_python.nf.output(...)
  • All major native data types (lists, dicts, etc.) are supported.
# example_script.py
from nf_python import nf

# Access arguments and options
print(nf.args)
print(nf.opts)

# Assign output
nf.output(result=nf.args[0] + 1)

Inline Code Support

pyFunction also support inline code. Here is an example:

result = pyFunction("""
    # Code is automatically de-indented correctly
    # `nf_python.nf` is accessible as `nf`
    nf.output(arg1=123, arg2='abc')
""")
assert result == [arg1: 123, arg2: 'abc']

result = pyFunction("""
    nf.output(arg1=123, arg2='abc', arg3=nf.args['foo'])
""", foo: 1)
assert result == [arg1: 123, arg2: 'abc', arg3: 1]

Contributing

Contributions and feedback are welcome! This project is in a preliminary exploration stage and lots of possible functionality remains to be added.

Install from source

If you want to build and run this plugin from source, you can use this method:

git clone git@github.com:royjacobson/nf-python.git && cd nf-python
make install
export NXF_OFFLINE=true
nextflow my_flow.nf -plugins "nf-python@0.1.4"  # Change appropriately

License

See COPYING for license information. The layout of the project is based on the nf-hello project, licensed under the Apache License 2.0.