example2

Build and deliver Nextflow module containers

Summary

This example shows how to associate a Dockerfile with a Nextflow module.

When executing a pipeline script enabling the Wave plugin, the Dockerfile is uploaded to the Wave service, a container is built on-the-fly, and pushed to a temporary repository. The container name is automatically included in the process execution and used to run the task.

Pipeline script

The pipeline script includes a simple module and uses it in the workflow:

include { hello } from './modules/foo'

workflow {
  hello()
}

Module script

process hello {
  debug true
  """
  cowsay Hello Summit! 
  """
}

Note: the process does not need to declare any container to used. Instead, a Dockerfile is included in the module directory.

Dockerfile

The Dockerfile defines the software to be installed.

FROM alpine 

RUN apk update && apk add bash cowsay \
        --update-cache \
        --repository https://alpine.global.ssl.fastly.net/alpine/edge/community \
        --repository https://alpine.global.ssl.fastly.net/alpine/edge/main \
        --repository https://dl-3.alpinelinux.org/alpine/edge/testing

Run it

nextflow run demo.nf -with-wave