/docker_nextflow

Container for running Nextflow (http://nextflow.io)

Primary LanguageDockerfile

Nextflow

A Squonk-compliant Nextflow container image.

You can use Docker's build-args to build the image for a specific nextflow release: -

$ V=20.07.1
$ docker build --build-arg NF_VERSION=$V -t informaticsmatters/nextflow:$V .
$ docker push informaticsmatters/nextflow:$V

Runtime configuration

The container image behaviour is configured with a number of environment variables: -

  • NF_REPORT_OPTIONS Reporting options with a default value of default -with-trace

  • NF_PROFILE_NAME The name of the profile (defined in nextflow-config) to execute. Docker execution would typically use the default (standard) but OpenShift execution would probably use kubernetes

  • NF_OPTIONS Additional options passed to the nextflow command-line. Default is an empty string ('')

  • NF_INIT_SCRIPT The name of a pre-nextflow script to run, default of nextflow-init.sh. The script has to be injected into the work-directory of the container (there isn't one by default). The script is run if it is found to exist.