README.md

Build and deliver Nextflow module containers to a private repository

Summary

This example shows how to associate a Dockerfile to a Nextflow module and push it to a preferred private repository.

When executing a pipeline script with the Wave plugin enabled, the Dockerfile is uploaded to the Wave service, a container is built on-the-fly, and pushed to the repository you have specified.

The repository access key needs to be provided using the Tower credentials associated with your own account.

To access your Tower account, specify your Tower access token in the Nextflow config file (see below).

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 be used. Instead, it references the Dockerfile 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

Nextflow config

docker { 
  enabled = true
} 

wave { 
  build.repository = 'docker.io/pditommaso/cowsay-demo'
}

tower {
  accessToken = "$TOWER_ACCESS_TOKEN"
}

The docker scope is only needed to run the example in your local computer using Docker.

Note: the user of the build.repository setting to push the container image built by Wave to your own repository. Replace the repository name with one of your choice.

Run it

nextflow run demo.nf -with-wave