NextflowWorkbenchLogo-2We have released NextflowWorkbench 1.3. This new release makes it easier to create frozen docker images with the bioinformatics resources needed by your analysis pipeline. Creating frozen images is useful in two situations:

  1. You are organizing training sessions to show others how to use a workflow and you need a simple way for trainees to install all the required software. Creating a frozen docker image that includes all the dependencies, from software to data indices will help you save time. Trainees download the image and are ready to go without lengthy configurations.
  2. You need to create a frozen analysis pipeline for a clinical data analysis pipeline (i.e., in the context of CLIA and/or New York State clinical test regulations). You can package the workflow and its dependencies in a docker image that can be tagged and represents a frozen state of the software and data.

Creating such a frozen image got easier with release 1.3 of the NextflowWorkbench. You can use a special instruction (install gobyweb artifacts) inside the Dockerfile and declaratively indicate which resources are needed, as shown in this snapshot:

Installing_GobyWebResources_Inside_A_Docker_Image

If you have defined this resource declaration in a Process or Bash script, you can simply type “install gobyweb artifacts” in the dockerfile and paste the resource bit of the statement (copy it from the script).

This special instruction will expand into a series of shell instructions that will install the requested software inside the image. The Process or script, when run, will automatically detect that the resources are present in the image and will run much faster, as these resources will not be installed again.

The following improvements are also included in release 1.3:

  • Improved auto-completion for artifact paths and paths inside the docker image (for instance, auto-completion will now warn you if the interactive container is not running).
  • Provide the ability to specify a current directory for interactive containers, so that relative path auto-completion knows what suggestions to offer when auto-completion is invoked.
  • Add Salmon 0.5.0 to the list of resources that can be installed as a GobyWeb resource.