«Worfklow» has been renamed «protocol list»

This section is outdated. We have renamed "workflows" (meaning an applied sequence of protocols) to "protocol list". LabID now uses the term "workflow" to refer to data analysis workflows.

Hands-on: Working with Workflow Templates

• 15 min
• Medium

Overview

In the previous tutorials, we learned how to link one or more protocols to a sample and mentioned that, such an ordered list of protocols is named a workflow. When you add protocols in the sample's workflow property, a sample-specific workflow is created automatically, in the background. Although you don't really need to know much about this workflow concept to work with LabID, it is better to understand what happens under the hood to avoid surprises and have a better experience.

Walkthrough

This hands-on makes use of material generated in previous hands-ons of this Biomaterial Management chapter. Please make sure to perform those before starting this exercise.

Step 1. What are those sample-specific workflows?

In the first Biomaterial hands-on , we linked two protocols to a sample named TXX_embryos_09-25-22_E25 (with XX being your trainee number e.g. T10_embryos_09-25-22_E25 for trainee10).

• Navigate to the Biomaterial menu and click the Sample sub-menu to bring the sample list. Make sure to display only your sample by setting the ownership filter to Personal . Locate the T10_embryos_09-25-22_E25 in the list (use the Name filter available in the column header if needed) and notice the Workflow: 2 steps link in the Workflow column (red arrow).

  Automatic naming of sample specific workflows

  

  The Workflow column of the sample table actually links to a workflow page.

• Click on this Workflow: 2 steps link to open the workflow detail page. This is a sample-specific workflow as stated by the Is Template negative value.

  The workflow detail page

  

• The page offers an Edit , click it, modify the workflow name (e.g. polyA RNA isolation from Zebrafish embryos) and Save. This results to an error!

  Sample-specific workflow cannot be changed from the workflow edit page

  

  Error when trying to edit a non-template workflow

Why can't we change the workflow details?

Imagine that you performed an experiment with 10 samples following a 2 steps-workflow (2 protocols) that you linked to all 10 samples (as we did for TXX_embryos_09-25-22_E25). In other words, you have 10 samples exactly like your TXX_embryos_09-25-22_E25.

The situation can be represented like on the below picture

Relationships between Samples, Workflows & Protocols

Each sample has its own workflow. Workflows reference protocols.

Editing the content of a protocol impacts all the samples since a workflow only links to the protocols. Conversely, editing a sample-specific workflow (e.g. removing one protocol) only affects one sample. This last behavior might not be expected by most users explaining why LabID blocks the edition of sample-specific workflows and only allows such modifications through the sample edit page (and batch edit operations).

• Navigate to the Protocols menu and click the Workflow sub-menu and click on New workflow

• Fill in the form and click Save item:

  • Name: polyA RNA isolation from Zebrafish embryos (trainee10) (replace with your real trainee number)
  • Protocols: select Zebrafish Embryo Production By In Vitro Fertilization then Poly(A) mRNA isolation
  • Notice how the Is Template is set to true (and can't be modified)
  Creating a Workflow template

  

  A workflow template is only a name, a list of protocols and an optional description.

Why can't we change the Is Template property?

For the same reason explained above: a sample-specific workflow must be created and modified through the sample's workflow property. Only template workflows can be directly modified.

• Navigate to the Biomaterial menu and click the Sample sub-menu to bring the sample list. Make sure to display only your sample by setting the ownership filter to Personal .

• Open the detail page of the s_condition_1_DAPI sample (that you must have created in the previous hands-on), switch to edit mode with Edit and set the workflow using the Select protocols from template option to polyA RNA isolation from Zebrafish embryos (trainee10)

  Setting sample's protocols using a workflow template

  

• Save and get back to the sample list page

How is the workflow for s_condition_1_DAPI sample named?

It is also named Workflow: 2 steps and not polyA RNA isolation from Zebrafish embryos (trainee10). This is because the workflow template has been duplicated into a sample-specific workflow which is, as usual, named automatically.

• Select all the samples whose name starts with s_pooled (they should all lack a workflow; you may use a filter on name as in below picture) and bring up the batch editor using

  Setting sample's protocols using a workflow template in batch

  

• In the batch editor pop-up, select Workflow in Attribute and set the workflow using the Select protocols from template option to polyA RNA isolation from Zebrafish embryos (trainee10). Confirm your choice on the warning, click Save and close the batch editor.

  Setting sample's protocols using a workflow template in batch

  

• Navigate to the Protocols menu and click the Workflow sub-menu. Make sure to display only your workflows by setting the ownership filter to Personal . All your sample-specific workflows are listed, all with similar names. With time, this may represent a lot of workflows. As we saw earlier these workflows can only be modified from the sample page. They are not identifiable by their name and are not linked to their sample (there is no e.g. linked sample column). You may prefer to ignore the non-templated workflows by removing them from your default workflow list display.

  Workflow list page polluted with sample-specific workflows

  

• Set the column filter Is Template on Yes (red arrow) and click the (boxed in red)

  Saving new default for the Workflow list page

  

  Saving a new page customization includes column filters

You now have a workflow page that will only list workflow templates.

Tip

To check your new workflow list page default display, copy the page URL, open a new browser window and paste the URL in the navigation bar.

Congrats! You have completed this hands-on. Next we will learn advanced tricks to manipulate samples in batch.