/nextflow-demos

Example Nextflow pipelines and programming techniques

Primary LanguageNextflowGNU General Public License v3.0GPL-3.0

nextflow-demos

Demonstrations of various programming techniques for use inside Nextflow pipelines. This repository is meant to be a supplement to the official Nextflow documentation (links below).

Install

Clone this repo:

git clone git@github.com:stevekm/nextflow-demos.git
cd nextflow-demos

Contents

Each subdirectory contains files to run sample Nextflow pipelines.

Files

  • Makefile: shortcut to commands to install and clean up Nextflow and its pipeline output

  • main.nf: Nextflow pipeline file

  • nextflow.config: config file for Nextflow pipeline (optional)

Sample Pipeline Directories

(listed in recommended order for new users)

  • print-samples: Prints samples from a list to the terminal

  • make-files: Creates files based on sample ID inputs

  • output-files: Same as make-files but includes custom file output options

  • async: demonstration of asynchronous process execution

  • custom-email-output: Creates files from sample ID's then sends the user an email with a pipeline summary and files attached

  • output-variable-name: Same as output-files but includes inline variable definition of output file names

  • R-Python: methods for using other scripting languages inside the Nextflow pipeline

  • join-pairs: joining pairs of samples based on ID across input channels

  • parse-samplesheet: parsing of a samplesheet as input for Nextflow pipeline

  • reporting: execution of Nextflow pipeline with reporting and config features enabled.

  • profiles-Docker-module: usage of 'profiles' to change process execution behavior to use Docker or environment modules

  • Groovy-code: example of using inline Groovy code inside the Nextflow pipeline

Usage

You can use the following commands inside the provided demo subdirs to run the demo pipelines.

Install Nextflow

# in a subdir in this repo
make

Run pipeline

./nextflow run main.nf

or

make run

Cleanup

make clean

Resources

Examples