gmhhope/nextflow-demos

Example Nextflow pipelines and programming techniques

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).

• an overview presentation about Nextflow can be found here (view here)

• Nextflow HTML report examples can be found here:

  • pipeline report

  • timeline report

NOTE: Some of the techniques demonstrated here may be deprecated by the new DSL2 syntax offered by Nextflow. Be sure to check that out as well.

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

• Nextflow Homepage: https://www.nextflow.io/

• Nextflow Docs: https://www.nextflow.io/docs/latest/getstarted.html

• Nextflow Patterns: https://nextflow-io.github.io/patterns/index.html

• Nextflow GitHub: https://github.com/nextflow-io/nextflow

• Nextflow Google Group: https://groups.google.com/forum/#!forum/nextflow

Examples

• Nextflow tutorial: https://github.com/nextflow-io/hack17-tutorial

• Nextflow examples: https://github.com/nextflow-io/examples

• Pipeline examples: https://github.com/nextflow-io/awesome-nextflow

• Boilerplate example for writing pipelines: https://github.com/stevekm/nextflow-boilerplate

• NYU pipelines:

  • exome sequencing: https://github.com/NYU-Molecular-Pathology/NGS580-nf

  • demultiplexing: https://github.com/NYU-Molecular-Pathology/demux-nf