Glad this is helping!
To edit a workflow, we have a walk-through here → Hands-on: Creating, Editing and Importing Galaxy Workflows / Creating, Editing and Importing Galaxy Workflows / Using Galaxy and Managing your Data
The UI has been updated, and that does not include many screenshots anyway, but maybe I can help more here.
First, know that workflows have versions that you can navigate. So, don’t be afraid to click on items and experiment. You can navigate everything you have done under the Changes icon in the far left menu.
Then, to edit a tool, start by clicking on the box for that tool in the editor. This will bring up the same tool form that you use when working directly in the history. This is loaded at the right side of the view. Using the icons at the top of that pop-out, you can expand to get the view in my screenshot. All of the tool form options can be modified here. Once you like the changes, save the workflow and run it. And, I didn’t mention this originally but you can modify reference genome choices at the workflow runtime too, on the workflow launch form.
That’s a lot! Here are some screenshots with those options. Maybe helps? Every workflow will be different of course, and tools themselves are different, but the basic portions about modifying the reference data is similar, as is the UI navigation.
Selecting a different reference genome in a workflow
Option 1: Modifying the reference genome used within the workflow in the editor (persistent changes).
Doing this means you only have to make the change once, since you will be saving the selection in your copy of the workflow.
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Click on the Workflow icon in the far left Activity Bar to view your listing. Search on this view as needed. You can explore and import public workflows here too!
On the card for the workflow, choose the Edit button.
- You can now make changes in your copy. Navigate by scrolling around, or using the lower right map, or even a web browser search as I did here (that is just a Chrome find search
command-fat the top in my screenshot).
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Click on the box for the tool you wish to modify.
In general, it is a good idea to start with the warning items reported by the content checker when you imported. Address those, then make any other changes that you want to.
Use the
minimizeandmaximizebuttons in the top corner if wanted. This was the part you were stuck at, yes? It is brand new so will not be in the tutorials/videos yet.
- Scroll down the form to the option you want to change.
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Once all the edits are complete, use the Save + Exit button.
Note: if you try to navigate away before saving, Galaxy will present a pop-up window to alert you about any unsaved changes! You can choose to just exit, and whatever the original state was will be unchanged. You can also use the Changes function to navigate what the changes are for review or to undo anything not wanted. You can also use this to double check that what you changed was only what you wanted to change!
I boxed in two other helpful functions you can explore later: Best Practices and Reports.
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You will now be back to the Workflow listing and exited from the editor.
From here, you can now try your updated workflow!
When using your own data with a new workflow, consider running a smaller representative dataset.
The tutorial data is one way to sort of “kick the tires” to flush out any problems.
Option 2: Modifying the reference genome used on the Workflow Launch view (runtime changes).
Doing this will mean that the changes are only applied for this specific workflow run.
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Starting at the Workflow Launch view.
This is the same view where the first method ends, and where the Run button for a workflow will always start.
You will be selecting your workflow inputs on this view, but you can also explore the workflow itself, and any items that can be modified at runtime will be presented.
The full view is collapsed. Use the link at the bottom to expand the details.
- Use the scroll bar to navigate down.
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From here, you can expand the individual tool steps.
The tool we are interested in has the reference genome option presented at the top with an Edit button.
- Clicking on Edit brings up the same tool form section we were using the editor, and you can search and select the same way to apply changes.
- The change is applied directly to this run (no “save” needed). You can also undo this if you want to start over.
- Once you are done making changes, scroll back up to the top.
Select your inputs as usual. Some servers will offer more complex ways to organize the run, too. Some even offer different different storage locations.
You can also do things like toggle the option to send the workflow outputs to a new history as I did in the screenshot. This puts all of the outputs and a clone of the inputs into a new history for you. I really recommend using this! It helps to keep things organized, but also can make any troubleshooting or changes easier to track.
The history will be named the same as the workflow by default but you can customize this. Everything will be timestamped as usual, along with all of the tool details, parameters, everything! You will be able to navigate the run in a History view, or under Workflow Invocations.
All the data will be exactly like working in a history directly. From here you can apply single tool runs, or use different tool runs, copy the data other places, download, etc. Nothing is static.
When you do want a persistent exact copy of the output, consider setting the history to an History → Archive status. This is a good choice for when the data will be shared in a publication or similar.
I hope this helps! The views here are newer so may not be captured exactly in the tutorials yet. Please let us know if this works or not for you! 