Modify a Public Workflow

User’s can make their workflows public, so that other CARMEN users may make use of them. However, there are a few things to note when trying this;

  1. You may not have sharing access for the input data files;
  2. You may not have sharing access for the services;
  3. You definitely won’t have access to the output folder, as it will point to the workflow owner’s own user space.

In the following example we will show you how to search for, edit and run a public workflow that you do not own. For the example, we will use a public workflow that we created to demonstrate the services and data prepared for the Retinal Waves Repository. This workflow generated a PDF plot from a single file that has been run through a burst detection service. To find this workflow, navigate to the workflows tab, and enter “Gigascience” in the search box – you should a service called “Quick Retinal Waves analysis workflow (Gigascience)” returned in the search results. Select this workflow and bookmark it so that it appears in your favourites folder.

As mentioned earlier, this workflow belongs to another user and refers to an output folder in their user space. The services and data files are public, so they can remain unmodified. However, we must edit the workflow so that the results of the workflow are placed in your own user space. To do this, load the workflow into the workflow editor.

workflow1
Load the workflow

This should display the graphical workflow editor, showing the tool chain and the connections. Note that there will be some Java interactions, so accept use of Java. The rightmost element, titled “Folder”, points to a folder in another user’s data space. Delete this folder by clicking on the “x” in the top-right hand corner of the folder element.

workflow2
Delete the output folder

The user must then add an output folder from their own data space. First, navigate to the data tab and select an output folder from within your own user space (1). Highlight the folder, and click on the “Add Folder” text button (2). Alternatively, create a new folder and add that to the workflow. The new folder box will appear on the workflow editor in the top left corner (3) of the workflow editor.

workflow3
Add a new output folder

Move the output folder into position on the workflow editor, and connect the service required service outputs to the folder. Connection is achieved by left-clicking on a connection node (as denoted by a black circle), and dragging the cursor to another connection node. In this case, we are only using the PDF file that is output from the plotting service. The other output, which in this case is a log file, and even intermediate results from the other services, can be connected to the output folder.

workflow4
Connect the new output folder

Note that there is a spanner icon in the top right hand corner of the three service boxes. Clicking on these allows the parameters for the service to be viewed, and edited. This can be used to re-run a workflow with different set of parameters.

Next, save the workflow, and close the workflow editor. The workflow can now be run and the results will be displayed in the log. Alternatively, you could construct your own workflow based on the services described above.