Pausing Workflows

By default, once executed, a workflow will run from one step to the next, all the way to the end without pause. If you want the workflow to stop, so that you can check progress or adjust input into a step, you will need to pause one or more of its steps. To pause a workflow step, click its node in the workflow panel and select Pause. To unpause a step, click its node again and select Resume.

Pausing a workflow to check progress:

1. From the Workflows page, select the desired workflow name. The workflow graph and its control buttons will open in the right panel. Don't forget to sign in to see your workflows.
2. In the workflow panel, click the step immediately following the step you want to check and select Pause. The paused step's color changes to purple. You can pause as many steps as you wish.
3. In the title of the workflow panel, click the Start button to the right of the workflow's name. The workflow begins to run.
4. Once the step you wish to inspect has completed, click its node and select More Info... to display its output. A window opens displaying information about that step:
   
   If the step is a tool step, input and output files may be viewed.
   
   Results of the most recent "Execute query" step are always displayed on the Extracts tab.
5. If you wish to continue running the workflow, click the paused step and select Resume. If you decide to stop, click the Reset button to return the workflow to its original waiting state.

Pausing a workflow to adjust input into a step:

In some situations, you might want to adjust a step's output before it is used as input into the next step. For example, suppose you've created a workflow that aligns a set of sequences. Rather than using the same sequences every time, you might want to stop the workflow and select new sequences each time the workflow runs. To do so:

1. From the Workflows page, select the desired workflow name. The workflow graph and its control buttons will open in the right panel. Don't forget to sign in to see your workflows.
2. In the workflow panel, click the step immediately following the step you want to adjust and select Pause. The paused step's color changes to purple. You can pause as many steps as you wish.
3. In the title of the workflow panel, click the Start button to the right of the workflow's name. The workflow begins to run.
4. Once all of the steps prior to the paused step have finished executing, click the Extracts tab to display the previous step's output.
   
   If the previous step is an "Execute query" step, you'll see query records. Use the "Select Records" and "Keep Only Selected Records" buttons to select the records that you want to input into the paused step.
   
   If the previous step is a Tool step that places its results on the Extracts page (not every tool does this), you'll see tool results. Use the "Select Records" and "Keep Only Selected Records" buttons to select the records that you want to input into the paused step.
5. Once you've finished adjusting input, return to the Workflows page, click the paused step and select Resume to continue. The workflow will begin to run.