Execute DNF Workflow

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This guide is intended for Biosustain DNA Foundry team.

🎯 This guide will show you how to execute Workflows submitted by researchers (or yourself) at Biosustain. Follow this guide if you need to create a Workflow instead.

What is a Benchling Workflow?

A Benchling Workflow contains:

  • details of the samples to be analysed

  • details of the analysis to be performed (in this case only Nanopore sequencing is available)

  • details of who submitted the Workflow

📩 Check your inbox for new submissions

As an Analyst, you will receive an email notification once a new Workflow is created (you will receive notifications only for the Workflow you are responsible for).

Access the submitted Workflow

Click on the link provided in the email. Example:

access the workflow

📆 Update the Workflow status to “Planned”

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If you are the person who created the workflow, you can skip this step.

When you are about to start the analysis, you can update the Workflow status to “PLANNED” to let the researcher know you are on it.

We suggest to use the status “Planned” instead of “In progress” because this enables for a more straightforward execution of the workflow later-on.

To udpate the status, go the the “Tasks” table, click “Edit”, and edit the “Status” column. Now click “Submit” to save the edit.

update the status of the workflow

Execute the Workflow

When you are ready to register all relevant information about the analysis run (either before or after the analysis is done), you can click on the “Execute” blue icon.

execute workflow

Create new Execution Entry

In the pop-up windown that showed up click “Execute” again, and a new Notebook Entry (from Template) will be automatically created. Follow the steps in the Notebook Entry to register the relevant information regarding the analysis run.

Submit the Output table

After adding the relevant information in the various tables of the Notebook Entry, you can fill in the Output table, for example adding the link to the Output folder where the data can be found and accessed.

submit output

Submitting the Output table will automatically change the status of the Workflow task to “Completed”.

The submitter will now receive a notification that the analyis is completed and the results ready to be accessed.