Modifying Workflows

This section describes how to change a workflow step's modifiable settings, so that you can repeat the workflow on different data or with modified parameters.

WARNING: Changes are permanent. Before you modify a workflow, you may want to make a copy, so that you don't overwrite the original workflow.

To make a copy of an existing workflow. This option works for public workflows and your own private workflows:

  1. Turn recording on so BioExtract Server can record what you do. To do so: Click the Workflows tab.
  2. At the top of the left panel, select Create and Import Workflows (only visible when signed in). The Create and Import Workflows form opens in the right panel.
  3. In Create Workflow at the top of the form, click the Record Workflow button.
  4. Next, open the workflow you want to make a copy of and run it. The BioExtract Server will record the running workflow in the background.
  5. When all of the steps in the workflow have completed, save a copy of the executed workflow. To do so: Select Create and Import Workflows at the top of the Workflows list. The Create and Import Workflows form will open in the right panel.
  6. In the Save Workflow section, type a new Name and keep or change the Description.
  7. Click the Save button. You'll see the copied workflow at the bottom of the Workflows list. You can now modify the original or the copy.

To modify a workflow step's settings:

  1. From the Workflows page, expand the workflow you want to modify by clicking the plus sign to the left of the workflow name. This will show you all of the steps included in that workflow. Don't forget to sign in to see your workflows.
  2. Next, expand the step you want to modify by clicking the plus sign to the left of the step name (like Query or Run tool ClustalW). The selected step expands and displays modifiable sub-steps (like Query and Tool):

    If you want to change the query request, click the plus sign to expand the Query step and click Query. A Query Information form opens in the right panel. You can change the search field and the search term. Click the Save button to keep your changes.

    If you want to change tool parameters, click the plus sign to expand the Run tool step and click Tool. The tool form opens in the right panel. Change parameters according to your data and preferences. Click the Save button to keep your changes.

    Some Tool sub-steps also have modifiable Input Data sections. If a Tool sub-step does not allow for input changes, then the Input Data section will not appear.

To verify your changes, run the modified workflow:

  1. Return to the Workflows list and select the modified workflow's name. The workflow graph and its control buttons will open in the right panel.
  2. In the title of the workflow panel, click the Start button to the right of the workflow's name. The workflow begins to run. Now wait.
  3. Once the workflow completes, check the workflow report for errors. To do so, click the Provenance button located below the workflow graph. Check the areas where changes were made for errors. Check the input and output files to make sure the correct data is being passed through the workflow.
  4. If errors occurred, troubleshoot and fix any problems. If the workflow still doesn't work, contact us through BioExtract Server feedback! in the top right corner of every page.