Nextflow

Nextflow is a free and open-source software used to write, deploy and share data-intensive, highly scalable, workflows on any infrastructure.

Compatibility

Our containerized methods are compatible with the Nextflow Domain Specific Language (DSL). It is possible to integrate the Containerized Data Science (CDS) CLI commands in Nexflow scripts, if the JSON parameters and data are available. For example, to run the histogram examples in rugplot: Histograms, a Nexflow script should be written as follows:

process rugplotviz {
  output:
    stdout

  """
  echo $PWD
  docker run --rm -v "$PWD":/app/data -u \$(id -u):\$(id -g) venustiano/rugplot:0.1.0 \
  plot -p histogram --file histogram_params.json
  """
}

workflow {
  rugplotviz | view { it.trim() }
}

Note that the latter two $ in the docker command are escaped. See the Nextflow documentation for further details.