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Nextflow and Jupyter Labs

By Stephen Rudd
Published in Articles
February 09, 2022
2 min read

We are pleased to introduce an update to our EPI2ME Labs product that now includes the functionality to launch our Nextflow pipelines directly from the EPI2ME Labs session. These new capabilities have been implemented to facilitate the launching of integrated workflows in an efficient manner whilst avoiding the requirement for using a terminal session.

Getting started

Install the new version of the EPI2ME Labs Launcher; this can be downloaded from our Downloads page. The LabsLauncher interface is largely unchanged – there is one small, but critical, requirement – we need to specify the path to the Nextflow binary.

jupyterflow
Figure 1. To set the Nextflow path, open the EPI2ME Labs Launcher 'Settings' dialog and enter the path into the 'nextflow_path' field. In the figure above the nextflow binary is located within the author’s Documents folder. More information on the Nextflow installation may be found in the EPI2ME Labs Workflows quickstart guide.

The new EPI2ME Labs landing page

When EPI2ME Labs is launched a new landing page is now presented. The landing page still provides the list of recently opened and available tutorials but now also provides a link to the EPI2ME Labs Workflows. The landing page is shown in Figure 2.

landing-page
Figure 2. EPI2ME Labs now has an updated landing page that is presented in your web browser. This still provides access to the recently run and other available tutorials (or notebooks as they are referred to in the Jupyter environment). EPI2ME Workflows can be selected by clicking on the 'Workflows' link provided in the navigation bar at the top of the screen.

When the “Workflows” link is selected from the navigation bar at the top of the landing page, the available workflows will be presented. The workflows page also shows the list of workflows that have been run, or are still running. Figure 3 shows a screenshot of the Workflows page – this shows three of the available workflows that may be selected and shows that one workflow, ArabidopsisSeq is currently running.

workflows-page
Figure 3. Screenshot showing the EPI2ME Labs workflows page. This page shows both available workflows and a history of workflows that have either been run in the past or are currently running on the host computer system.

Running a workflow

To run a workflow is now simple: select a workflow from the list of available workflows. This will open a new dialog page that will encourage you to specify a nextflow analysis. Figure 4 shows how an analysis can be built for the wf-alignment workflow – we need to specify both the collection of FASTQ files to map and the FASTA format reference genome. The analysis is started with a click of the “RUN COMMAND” button and the analysis will commence.

workflow-options
Figure 4. Selecting the wf-alignment workflow presents a dialog that asks for the relevant experimental parameters. This includes the starting FASTQ sequences (under Input/output options, not shown) and the reference genome sequence. Starting the analysis is performed by clicking on the 'RUN COMMAND' button shown at the bottom of the screen.

Once a workflow has been started the experiment information becomes available as a workflow instance. Each instance has its own page and this provides both the output from the Nextflow command, links to the result files and additional metadata on the version of the workflow called, the parameters passed and the actual command run on the computer. Figure 5 shows an example of a workflow instance screen for the wf-alignment workflow that we have building.

workflow-instance
Figure 5. Screenshot taken from the workflow instance report for an analysis that is running. The report shows the parameters that have been passed to the workflow, the intermediate output from the Nextflow command (and potentially error messages) and the result files (bottom panel).

When the analysis has completed the results are made available through the same instance report page. The analysis report is accessible by clicking on the “OPEN REPORT” button.


Tags

#nextflow#jupyter#workflows
Stephen Rudd

Stephen Rudd

Bioinformatics product manager

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