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Add a tutorial section for renaming sub-WF outputs #5162

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Add a tutorial section for renaming sub-WF outputs #5162

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Add a tutorial section for renaming sub-WF outputs
RZ9082 Jul 15, 2024
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RZ9082 Jul 15, 2024
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Merge branch 'main' into renaming-sub-wf-outputs
shiltemann Dec 6, 2024
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42 changes: 42 additions & 0 deletions topics/galaxy-interface/tutorials/workflow-parameters/tutorial.md
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Expand Up @@ -19,6 +19,7 @@ key_points:
contributors:
- mvdbeek
- hexylena
- RZ9082
level: Intermediate
subtopic: workflows

Expand Down Expand Up @@ -222,6 +223,7 @@ In this example we will construct a workflow where we calculate the sum of all v

With this you're ready to run the workflow!

> <a name="running-the-workflow-2"></a>
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> <hands-on-title>Running the workflow</hands-on-title>
>
> 1. Upload a dataset using "Paste/Fetch data" with the contents, and set the filetype manually to "tabular" during upload
Expand Down Expand Up @@ -260,6 +262,46 @@ the first column.
> `Parse parameter value` tool on it, running all downstream tools once for each parameter.
{: .tip}

# Rename sub-workflow outputs utilizing workflow variables

Oftentimes it is useful to use variables enabling users to determine text inputs, queries, output names, etc.
This approach is particularly beneficial when employing sub-workflows, such as when a sub-workflow is used multiple times and each instance requires a unique output name.
In the following example we will construct a straightforward workflow, and utilize variables to facilitate the renaming of outputs when running the workflow.

> <hands-on-title>Construct sub-workflow utilizing variables to rename outputs</hands-on-title>
>
> 1. {% icon galaxy-wf-new %} Create a new workflow and choose a unique name for it
> 2. Add an **input dataset** {% icon tool %}
> 3. Add **Add column** {% icon tool %} to the workflow
> - Connect **Input dataset** to {% icon wf-input %} **to Dataset**
> - Click on **Add column** and scroll down the right panel
> - Open the **Configure Output: 'out_file1'** section
> - Write `${my label}` into **Rename dataset**
> 4. Add an **input parameter** and give it the label `my label` (Leave it unconnected)
> 5. {% icon galaxy-save %} Save the workflow
{: .hands_on }

> <hands-on-title>Construct main workflow</hands-on-title>
>
> 1. {% icon galaxy-wf-new %} Create a new workflow and choose a unique name for it
> 2. Scroll the left sidebar down, click on **Workflow**, and add the sub-workflow created in the steps above twice
> 3. Add 2x **input parameter** {% icon tool %}
> - Name the first one `First workflow output name` and connect to {% icon wf-input %} **my label** in the first sub-workflow
> - Name the second one `Second workflow output name` and connect to {% icon wf-input %} **my label** in the second sub-workflow
> 4. Add an **input dataset** {% icon tool %} and connect it to both {% icon wf-input %} **Input dataset** of the sub-workflows
> 5. {% icon galaxy-save %} Save the workflow
{: .hands_on }

> <hands-on-title>Running the main workflow</hands-on-title>
>
> 1. Upload/reuse the tabular file from the following [section](#running-the-workflow-2)
> 2. Navigate to Workflow tab
> 3. Click on {% icon workflow-run %} **Run workflow**
> 4. Select the tabular file as your input
> 5. Define the name you want for your first and second output datasets
> 6. {% icon workflow-run %} Run the workflow
{: .hands_on }

# Conclusion


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