We have released version 1.2.0 or the NextflowWorkbench. This is a major release that includes:

  • Languages that provide a docker IDE,
  • Languages to easily install tens of bioinformatics tools useful for high-throughput sequence data analysis.

This post gives an overview of the docker IDE features. We have added two new Chapters to the documentation booklet [Tablet, PDF]. Please see the updated doc for details.

Docker IDE

Nextflow supports docker containers, but the construction of suitable Docker images is necessary to customize the tools available to the workflow, and if you are new to docker, using its command line interface is not particularly user-friendly. The workbench now offers a language to configure and build images from Dockerfiles:

NextflowDockerfiles

In the snapshot above, you can see this language used to describe how a centos base image should be created. The light-bulb provides intentions to merge two successive RUN commands. (You can of course customize intentions to support your workflows since this language is fully extendable in MPS). Clicking on the Build image button will instruct docker to construct the image. You can follow the build process directly within MPS (in the info message tab). When the process succeeds, an image root node is created:

ImageRootNode

This node links the image back to the docker file that was used to create it. The image is added to the list of images built with the Dockerfile (shown at the top of the previous figure). Using the image root node, you can tag, push to a docker registry or run a container.

Once the image is ready, or available in Docker Registry (e.g., Docker Hub), you can use it to execute a BASH script or a Nextflow Process:

RunBashInsideContainer

More than this, the container can be started for interactive use. This makes it possible for a user to interactively peek at the filesystem in the container:

VisualizingFilesInTheRunningContainer

 

This makes it a bit easier to figure out where files are inside the container filesystem. The next post will describe the features introduced in release 1.2 of interest to bioinformaticians.