Nextflow WR

Nextflow extension module for wr

This allows submitting jobs to LSF while taking advantage of LSF job arrays, and to an OpenStack cluster with autoscaling up and down.

Install

The module is not yet available in Maven. In the mean time, you can build it yourself:

git clone https://github.com/nextflow-io/nf-wr.git
cd nf-wr
make assemble
export NXF_CLASSPATH=$PWD/build/libs/nf-wr-1.0.0.jar

Usage

To enable this executor set the property process.executor = 'wr' in the nextflow.config file. See wr's wiki for more details.

The pipeline can be launched either on a local computer or an OpenStack instance.

To start running wr, install wr by downloading it, unzipping it and optionally placing it in your $PATH. Then for LSF usage run:

wr manager start -s lsf

For OpenStack usage, additionally source your OpenStack credentials "rc" file and run:

wr cloud deploy

Your options to "deploy" or your wr configuration determine the default image and allowed flavors that will be used to run tasks. Amongst the allowed flavors, wr will pick the smallest flavor that is large enough to run your tasks, according to the cpu, memory and disk requirements of each task.

When using OpenStack without a shared disk, an S3 bucket must be used as pipeline work directory and for pipeline file inputs. This means nextflow must be configured with access details of your S3 system, and wr must also be aware of those details. This can be arranged most easily by having an ~/.s3cfg file (the file you would need for the s3cmd tool).

Dir structure

• src/main: Module source files
• src/resources: Module non source resources
• src/test: Module unit test sources