Repository: galaxyproject/training-material
Pull request #5946: **Ready for Review** | galaxy-intro-101 tutorial |updated the workflow, tutorial, tools, and text.
Author: login: dadrasarmin
Labels: name: introduction
name: faqs
Created: 2025-04-11T10:02:21Z | Merged: 2025-04-22T06:35:00Z

I have followed the steps as described [here](https://training.galaxyproject.org/training-material/topics/contributing/tutorials/updating_tutorial/tutorial.html).

1. I updated the workflow and tested it based on the suggestions [here](https://training.galaxyproject.org/training-material/faqs/gtn/gtn_workflow_testing.html) and [here](https://training.galaxyproject.org/training-material/topics/contributing/tutorials/updating_tutorial/tutorial.html).
2. I updated the tutorial text.
3. I imported the new workflow into usegalaxy.(org,eu,org.au,fr) and checked whether it works or not. I added the archived histories as input history and answer key as explained [here](https://training.galaxyproject.org/training-material/topics/contributing/faqs/input-and-answer-keys.html).
4. I updated the screenshots to match the new UIs.
5. I removed a file in the `workflows` directory because I think it was related to old versions of Planemo.
6. I hosted the GTN locally and it seems fine.
7. When I check the workflow button using the local build, I do not know why it still shows the old workflow. Is something wrong there?

Since this is a tutorial for new users, I hope I have not broke something that was working. This is the first time that I am doing this. I highly appreciate it if someone could review and tell me if I have done something wrong and how to do it better.

Thanks!
Armin



Diff:
diff --git a/faqs/gtn/gtn_workflow_testing.md b/faqs/gtn/gtn_workflow_testing.md
index c51b291761ef83..da63c51feb1416 100644
--- a/faqs/gtn/gtn_workflow_testing.md
+++ b/faqs/gtn/gtn_workflow_testing.md
@@ -10,14 +10,14 @@ contributors: [hexylena]
 
 1. Find a tutorial that you're interested in, that **doesn't currently have tests.**
 
-   This tutorial has a workflow (`.ga`) and a test, notice the `-test.yml` that has the same name as the workflow `.ga` file.
+   This tutorial has a workflow (`.ga`) and a test, notice the `-tests.yml` that has the same name as the workflow `.ga` file.
 
    ```
    machinelearning/workflows/machine_learning.ga
-   machinelearning/workflows/machine_learning-test.yml
+   machinelearning/workflows/machine_learning-tests.yml
    ```
 
-   You want to find tutorials without the `-test.yml` file. The workflow file might also be missing.
+   You want to find tutorials without the `-tests.yml` file. The workflow file might also be missing.
 
 2. Check if it has a workflow (if it does, skip to step 5.)
 3. Follow the tutorial
diff --git a/topics/introduction/images/101_04.png b/topics/introduction/images/101_04.png
index e6f3fd31e5498d..8e922adb59cb29 100644
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diff --git a/topics/introduction/images/101_bed_intersect_interface.png b/topics/introduction/images/101_bed_intersect_interface.png
index 8983ee89ad9a7a..d26fa912af1392 100644
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diff --git a/topics/introduction/images/101_datamash_1.png b/topics/introduction/images/101_datamash_1.png
index dc74ef65a9a1a7..4560b8b135e791 100644
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diff --git a/topics/introduction/images/101_displayucsc.png b/topics/introduction/images/101_displayucsc.png
index f6c316bc8a7150..1e87d337db84bc 100644
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diff --git a/topics/introduction/images/101_rename.png b/topics/introduction/images/101_rename.png
index 69d5eaddec1cb0..16b5c07fb7b9a7 100644
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diff --git a/topics/introduction/images/configure_wf_output.png b/topics/introduction/images/configure_wf_output.png
index 26593561d10f71..4fa9bc47da2165 100644
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diff --git a/topics/introduction/images/drag_n_drop_dataset.gif b/topics/introduction/images/drag_n_drop_dataset.gif
index 94e9aa885ad943..798ae661254d89 100644
Binary files a/topics/introduction/images/drag_n_drop_dataset.gif and b/topics/introduction/images/drag_n_drop_dataset.gif differ
diff --git a/topics/introduction/images/galaxy_interface.png b/topics/introduction/images/galaxy_interface.png
index f9888ff84a562f..533dc3c00c62da 100644
Binary files a/topics/introduction/images/galaxy_interface.png and b/topics/introduction/images/galaxy_interface.png differ
diff --git a/topics/introduction/images/histories_side_by_side_view.png b/topics/introduction/images/histories_side_by_side_view.png
index 24b3fd57423604..1c0b2f3cb5a594 100644
Binary files a/topics/introduction/images/histories_side_by_side_view.png and b/topics/introduction/images/histories_side_by_side_view.png differ
diff --git a/topics/introduction/images/wf_editor_open.png b/topics/introduction/images/wf_editor_open.png
index 0bd1184ae94992..764f4b08880ff5 100644
Binary files a/topics/introduction/images/wf_editor_open.png and b/topics/introduction/images/wf_editor_open.png differ
diff --git a/topics/introduction/images/workflow_cards.png b/topics/introduction/images/workflow_cards.png
index 8bff8beadf175b..7c6bd258f22570 100644
Binary files a/topics/introduction/images/workflow_cards.png and b/topics/introduction/images/workflow_cards.png differ
diff --git a/topics/introduction/images/workflow_running.png b/topics/introduction/images/workflow_running.png
index 018515b64ea42b..1025230f3b97bd 100644
Binary files a/topics/introduction/images/workflow_running.png and b/topics/introduction/images/workflow_running.png differ
diff --git a/topics/introduction/images/workflow_setting_inputs.png b/topics/introduction/images/workflow_setting_inputs.png
index 5a9b62eb1d5277..095fcb4107518e 100644
Binary files a/topics/introduction/images/workflow_setting_inputs.png and b/topics/introduction/images/workflow_setting_inputs.png differ
diff --git a/topics/introduction/tutorials/galaxy-intro-101/tutorial.md b/topics/introduction/tutorials/galaxy-intro-101/tutorial.md
index 1cc33a02df36d3..49abff1d53af4c 100644
--- a/topics/introduction/tutorials/galaxy-intro-101/tutorial.md
+++ b/topics/introduction/tutorials/galaxy-intro-101/tutorial.md
@@ -33,6 +33,8 @@ contributions:
     - bgruening
     - pajanne
     - hexylena
+  editing:
+    - dadrasarmin
   funding:
     - psu
     - erasmusmc
@@ -58,7 +60,19 @@ recordings:
   - natalie-wa
   bot-timestamp: 1726511277
 
-
+answer_histories:
+- label: "usegalaxy.org"
+  history: https://usegalaxy.org/u/dadrasarmin/h/update-the-workflow-of-the-galaxy-basics-for-genomics
+  date: 2025-02-04
+- label: "usegalaxy.eu"
+  history: https://usegalaxy.eu/u/armin.dadras/h/galaxy-basics-for-genomics
+  date: 2025-02-04
+- label: "usegalaxy.fr"
+  history: https://usegalaxy.fr/u/armin.dadras/h/galaxy-basics-for-genomics
+  date: 2025-02-04
+- label: "usegalaxy.org.au"
+  history: https://usegalaxy.org.au/u/armin.dadras/h/update-the-workflow-of-the-galaxy-basics-for-genomics
+  date: 2025-02-04
 ---
 
 
@@ -110,7 +124,7 @@ The Galaxy interface consists of three main parts:
 3. Your analysis **History** is recorded on the right
 
 
-![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.svg "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
+![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.png "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
 {: .comment}
 
 
@@ -181,7 +195,7 @@ Below we describe how you can do this, but it is not necessary for this tutorial
 > >
 > >     ![`UCSC Main table browser` menu entry](../../images/101_01.png)
 > >
-> >     You will be taken to the **UCSC table browser**, which looks something like this:
+> >     When you click on this tool, you will be taken to the **UCSC table browser**, which looks something like this:
 > >
 > >     ![`UCSC table browser` tool, first screen for exons](../../images/101_02.png)
 > >
@@ -191,7 +205,7 @@ Below we describe how you can do this, but it is not necessary for this tutorial
 > >     - *"assembly"*: `Dec. 2013 (GRCh38/hg38)`
 > >     - *"group"*: `Genes and Gene Predictions`
 > >     - *"track"*: `GENCODE v36` (or a more recent version)
-> >     - *"table"*: `knownGene`
+> >     - *"table"*: `knownGeneV36`
 > >     - {% icon param-text %} *"region"* should be changed to `position` with value `chr22`
 > >     - *"output format"* should be changed to `BED - browser extensible data`
 > >     - {% icon param-check %} *"Send output to"* should have the option `Galaxy` checked
@@ -200,7 +214,7 @@ Below we describe how you can do this, but it is not necessary for this tutorial
 > >     > If the *"table"* drop down menu does not show the `knownGene` option. Set *"group"* to `All tables` and scroll down.
 > >     {: .comment}
 > >
-> > 2. Click on the **get output** button and you will see the next screen:
+> > 2. Click on the **Get output** button and you will see the next screen:
 > >
 > >    ![`UCSC table browser` tool, second screen for exons](../../images/101_03.png)
 > >
@@ -234,7 +248,7 @@ Below we describe how you can do this, but it is not necessary for this tutorial
 > We now have information about the exon locations, but our original question was which exon contains the largest number of SNPs, so let's get some information about SNP locations from UCSC as well:
 >
 > > <hands-on-title>Obtaining SNPs from UCSC</hands-on-title>
-> > Again open the `UCSC Main table browser` tool and set the following parameters
+> > Again, search for **UCSC Main table browser** Browser on the tools search bar {% icon tool %} and set the following parameters
 > >
 > > 1. **UCSC Main** {% icon tool %} table browser:
 > >    - *"group"* should be changed to `Variation`
@@ -245,7 +259,7 @@ Below we describe how you can do this, but it is not necessary for this tutorial
 > >
 > >    The *"track"* setting shows the version of the SNP database to get. In this example it is version 151, but you may select the latest one. Your results may vary slightly from the ones in this tutorial when you select a different version, but in general it is a good idea to select the latest version, as this will contain the most up-to-date SNP information.
 > >
-> > 2. Click on the **get output** button to find a form similar to this:
+> > 2. Click on the **Get output** button to find a form similar to this:
 > >
 > >    ![`UCSC table browser` tool, second screen for SNPs](../../images/101_07.png)
 > >
@@ -271,11 +285,11 @@ Our objective is to find which exon contains the most SNPs. Therefore we have to
 
 > <hands-on-title>Finding Exons</hands-on-title>
 >
-> To find intersection we will be using `intersect intervals` tool from [BEDTools](https://bedtools.readthedocs.io/en/latest/content/overview.html) package.
+> To find intersection we will be using `intersect intervals` {% tool [bedtools intersect intervals](toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0) %} from [BEDTools](https://bedtools.readthedocs.io/en/latest/content/overview.html) package.
 >
-> 1. {% tool [bedtools intersect intervals](toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1) %} the intervals of two datasets side-by-side:
+> 1. {% tool [bedtools intersect intervals](toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0) %} find overlapping the intervals in various ways:
 >
->    Enter the word `intersect` in the search bar of the tool panel, and select the
+>    If you opened the tutorial on any usegalaxy.* instance, you can click on the tool name and will open the correct tool with correct version. Or, you can search for this tool yourself. Enter the word `intersect` in the search bar of the tool panel, and select the
 >    tool named `bedtools Intersect intervals`
 >
 >    - *"File A to intersect with B"*: Select `Exons`
@@ -286,13 +300,13 @@ Our objective is to find which exon contains the most SNPs. Therefore we have to
 >    The interface of the tool should look like this:
 >    ![Bedtool intersect interval interface](../../images/101_bed_intersect_interface.png)
 >
-> 2. Click **Run Tool**
-> 3. Wait for the job to finish
+> 2. Click **Run Tool**.
+> 3. Wait for the job to finish.
 > 4. View the resulting file (with the {% icon galaxy-eye %} (eye) icon). If everything went okay, you should see a file that looks similar to this:
 >
 >    ![Contents of the `Join` output dataset](../../images/101_joined.png)
 >
->    Here column 4 contains exon IDs (e.g., `ENST00000252835.5_cds_0_0_chr22_15528159_f`) and column 10 lists SNP IDs (e.g., `rs9617249`) Remember that variations are possible due to using different versions of UCSC databases: as long as you have similar looking columns you did everything right!
+>    Here column 4 contains exon IDs (e.g., `ENST00000252835.5_cds_0_0_chr22_15528159_f`) and column 10 lists SNP IDs (e.g., `rs9617249`). Remember that variations are possible due to using different versions of UCSC databases: as long as you have similar looking columns you did everything right!
 >    > <tip-title>Where do I find tool documentation?</tip-title>
 >    > All Galaxy tools include documentation. If you scroll down on this page, you will find the help of the tool.
 >    {: .tip}
@@ -301,9 +315,9 @@ Our objective is to find which exon contains the most SNPs. Therefore we have to
 >    >
 >    > Did the Intersect tool error with a memory failure? Or is this step executing for a long time? Most likely a setting was missed when extracting the data from the UCSC Table Browser. Try again, double checking that:
 >    >
->    >  * For both SNP and EXON: *"region"* is actually changed to `position` with value `chr22`
->    >  * For EXON: *"Create one BED record per"* `Coding Exons` is selected (*not* `Whole Gene` as for the SNP data)
->    >  * Carefully inspect the remaining Table Browser settings if these two most common reasons for problems were correct in your tool executions
+>    >  * For both SNP and EXON: *"region"* is actually changed to `position` with value `chr22`.
+>    >  * For EXON: *"Create one BED record per"* `Coding Exons` is selected (*not* `Whole Gene` as for the SNP data).
+>    >  * Carefully inspect the remaining Table Browser settings if these two most common reasons for problems were correct in your tool executions.
 >    {: .comment}
 >
 {: .hands_on}
@@ -314,7 +328,7 @@ Let's take a look at this dataset. The first six columns correspond to the exons
 > For the first 3 exons in your file, what is the number of SNPs that fall into that exon?
 >
 > > <solution-title></solution-title>
-> > At the time of writing, for hg38/GENCODE v29, joined with "Common dbSNPs(153)", using <kbd>ctrl-f</kbd> (<kbd>cmd-f</kbd> on Mac OS) to look for how many times each is used:
+> > At the time of writing, for hg38/GENCODE v29, joined with "Common dbSNPs(153)", using <kbd>ctrl+f</kbd> (<kbd>cmd+f</kbd> on Mac OS) to look for how many times each is used:
 > >
 > > Gene | Occurences
 > > ---- | ----------
@@ -400,13 +414,13 @@ Let's say we want a list with just the top-5 exons with highest number of SNPs.
 
 > <hands-on-title>Select first</hands-on-title>
 >
-> 1. {% tool [Select first](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0) %} lines from a dataset (head):
+> 1. {% tool [Select first](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0) %} lines from a dataset (head):
 >
 >    - *"File to select"*: The output from **Sort** {% icon tool %} (previous step of the analysis)
 >    - "*Operation*": `Keep first lines`
 >    - *"Number of lines"*: `5`
 >
-> 2. Click **Run Tool**
+> 2. Click **Run Tool**.
 >
 > 3. Examine the output file, this should contain only the first 5 lines of the previous dataset.
 >
@@ -478,7 +492,7 @@ You can create as many histories as you want. If you create a new history, your
 
 ![Overview of histories with their datasets](../../images/histories_side_by_side_view.png "Histories side-by-side view: in this view you drag datasets between histories, switch between histories, create new histories etc.")
 
-You can always return to your analysis view by clicking on Home icon {% icon galaxy-home %} (**Analyze Data** on older versions of Galaxy) in the top menu bar.
+You can always return to your analysis view by clicking on Galaxy Icon in the top menu bar.
 
 ## Convert your analysis history into a workflow
 
@@ -510,9 +524,9 @@ Galaxy makes this very easy with the `Extract workflow` option. This means any t
 >
 >    You will get a message that the workflow was created. But where did it go?
 >
-> 6. Click on **Workflow** in the top menu of Galaxy. Here you have a list of all your workflows. Your newly created workflow should be listed at the top:
+> 6. Click on **Workflows** in the left menu of Galaxy (Activity Bar). Here you have a list of all your workflows. Your newly created workflow should be listed at the top:
 >
->    ![`Your workflows` list](../../images/workflow_cards.png "Workflow are listed in  the center pane of the Galaxy interface as cards.")
+>    ![`Your workflows` list](../../images/workflow_cards.png "Workflow are listed in the center pane of the Galaxy interface as cards.")
 {: .hands_on}
 
 ## The workflow editor
@@ -554,7 +568,7 @@ We can examine the workflow in Galaxy's workflow editor. Here you can view/chang
 >
 > 8. **Save your workflow** (important!) by clicking on the {% icon galaxy-save %} icon at the top right of the screen.
 >
-> 9. **Return** to the analysis view by clicking on the Home icon {% icon galaxy-home %} (or **Analyze Data** on older versions of Galaxy) at the top menu bar.
+> 9. **Return** to the analysis view by clicking on the Galaxy Icon at the top left of the menu bar.
 >
 {: .hands_on}
 
@@ -583,7 +597,7 @@ Now that we have built our workflow, let's use it on some different data. For ex
 >
 >    - Drag and drop `Exons` dataset into the empty history created at step 1
 >    ![Drag and drop of `Exons` dataset in the history overview](../../images/drag_n_drop_dataset.gif)
-> 3. Click the Home icon {% icon galaxy-home %} (or **Analyze Data** on older Galaxy versions) at the top to return to the main analysis window
+> 3. Click on Galaxy at the left to return to the main analysis window
 >
 > 4. {% tool [Upload Data](upload1) %} the Repeats file from [Zenodo](https://doi.org/10.5281/zenodo.4104428)
 >
@@ -639,13 +653,13 @@ Now that we have built our workflow, let's use it on some different data. For ex
 >    >  * If you see an "Invalid column choice" error, you need to specify which column you want to use. If you have to type the column number, you need to type just the number e.g. `4` (not `Column 4` or anything else).
 >    {: .comment}
 >
-> 8. Once the workflow has started, you will initially be able to see all its steps, but the unimportant intermediates will disappear after they complete successfully:
+> 8. Once the workflow has started, you will initially be able to see all its steps, but the unimportant intermediates may disappear after they complete successfully (based on the workflow settings):
 >
 >    ![Datasets appearing in the history](../../images/workflow_running.png)
 {: .hands_on}
 
 > <comment-title>Unhiding hidden datasets</comment-title>
-> Because most intermediate steps of the workflow were hidden, once it is finished you will only see the final two datasets. If we want to view the intermediate files after all, you can click the "## hidden" just below the history's name.
+> Because most intermediate steps of the workflow could be hidden, once it is finished you may only see the final two datasets. If we want to view the intermediate files after all, you can click the "## hidden" just below the history's name.
 {: .comment}
 
 > <question-title></question-title>
diff --git a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-test.yml b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-test.yml
deleted file mode 100644
index 6e9f5f6a845e7b..00000000000000
--- a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
----
-- doc: Test sample data for the workflow
-  job:
-    Exons:
-      class: File
-      location: https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-Coding-Exons.bed
-      filetype: bed
-    Features:
-      class: File
-      location: https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-dbSNP153-Whole-Gene-SNPs.bed
-      filetype: bed
-  outputs:
-    top_5_exons:
-      asserts:
-        has_text:
-          text: 'ENST00000253255.7_cds_0_0_chr22_46256561_r'
diff --git a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-tests.yml b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-tests.yml
new file mode 100644
index 00000000000000..7576cd7f76f927
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow-tests.yml
@@ -0,0 +1,13 @@
+- doc: Test sample data for the workflow
+  job:
+    Exons:
+      class: File
+      path: https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-Coding-Exons.bed
+      filetype: bed
+    Features:
+      class: File
+      path: https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-dbSNP153-Whole-Gene-SNPs.bed
+      filetype: bed
+  outputs:
+    top_5_exons:
+      path: test-data/top_5_exons.bed
diff --git a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.eu.json b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.eu.json
deleted file mode 100644
index 3a47997afdf5b1..00000000000000
--- a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.eu.json
+++ /dev/null
@@ -1,1012 +0,0 @@
-{
-    "summary": {
-        "num_errors": 0,
-        "num_failures": 0,
-        "num_skips": 0,
-        "num_tests": 1
-    },
-    "tests": [
-        {
-            "data": {
-                "end_datetime": "2023-05-18T19:40:47.480254",
-                "inputs": {
-                    "Exons": {
-                        "class": "File",
-                        "filetype": "bed",
-                        "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-Coding-Exons.bed"
-                    },
-                    "Features": {
-                        "class": "File",
-                        "filetype": "bed",
-                        "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-dbSNP153-Whole-Gene-SNPs.bed"
-                    }
-                },
-                "invocation_details": {
-                    "details": {
-                        "error_message": "",
-                        "history_id": "a7e26bbbb0830b20",
-                        "history_state": "ok",
-                        "invocation_id": "4e6187ae89df9163",
-                        "invocation_state": "scheduled",
-                        "workflow_id": "b9fe010bdb910e56"
-                    },
-                    "steps": {
-                        "0. Exons": {
-                            "action": null,
-                            "id": "137fffe5e92f37af",
-                            "job_id": null,
-                            "jobs": [],
-                            "model_class": "WorkflowInvocationStep",
-                            "order_index": 0,
-                            "output_collections": {},
-                            "outputs": {
-                                "output": {
-                                    "id": "4838ba20a6d86765828ccbcc3eb28a4b",
-                                    "src": "hda",
-                                    "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
-                                }
-                            },
-                            "state": "scheduled",
-                            "subworkflow": null,
-                            "subworkflow_invocation_id": null,
-                            "update_time": "2023-05-18T17:34:36.117311",
-                            "workflow_step_id": "47c79ce5a092d365",
-                            "workflow_step_label": "Exons",
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-                                        "header_lines": "\"0\"",
-                                        "order": "\"DESC\"",
-                                        "style": "\"num\""
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-                                    "stdout": "",
-                                    "tool_id": "sort1",
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-                                    "traceback": null,
-                                    "update_time": "2023-05-18T17:37:45.740051",
-                                    "user_email": "hxr@informatik.uni-freiburg.de"
-                                }
-                            ],
-                            "model_class": "WorkflowInvocationStep",
-                            "order_index": 4,
-                            "output_collections": {},
-                            "outputs": {
-                                "out_file1": {
-                                    "id": "4838ba20a6d867650b679d679c1fbabd",
-                                    "src": "hda",
-                                    "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
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-                            "workflow_step_label": null,
-                            "workflow_step_uuid": "4dd35991-4996-4f7d-8690-bde783f6fa6a"
-                        },
-                        "5. Unnamed step": {
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-                            "id": "06226aff05ce5d1f",
-                            "job_id": "11ac94870d0bb33ad12002ce0209213b",
-                            "jobs": [
-                                {
-                                    "command_line": "head --lines 5 '/data/dnb08/galaxy_db/files/c/8/b/dataset_c8b6796e-41f3-41de-9a94-82a3e7c388b7.dat' > '/data/jwd05e/main/060/036/60036243/outputs/galaxy_dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat'",
-                                    "command_version": "head (GNU coreutils) 8.25",
-                                    "create_time": "2023-05-18T17:34:36.414517",
-                                    "dependencies": [],
-                                    "exit_code": 0,
-                                    "external_id": "43511785",
-                                    "galaxy_version": "23.0",
-                                    "history_id": "a7e26bbbb0830b20",
-                                    "id": "11ac94870d0bb33ad12002ce0209213b",
-                                    "inputs": {
-                                        "infile": {
-                                            "id": "4838ba20a6d867650b679d679c1fbabd",
-                                            "src": "hda",
-                                            "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
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-                                    "job_messages": [],
-                                    "job_metrics": [
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-                                            "plugin": "hostname",
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-                                            "title": "hostname",
-                                            "value": "vgcnbwc-worker-c28m475-9359.novalocal"
-                                        },
-                                        {
-                                            "name": "galaxy_slots",
-                                            "plugin": "core",
-                                            "raw_value": "1.0000000",
-                                            "title": "Cores Allocated",
-                                            "value": "1"
-                                        },
-                                        {
-                                            "name": "galaxy_memory_mb",
-                                            "plugin": "core",
-                                            "raw_value": "3891.0000000",
-                                            "title": "Memory Allocated (MB)",
-                                            "value": "3891"
-                                        },
-                                        {
-                                            "name": "start_epoch",
-                                            "plugin": "core",
-                                            "raw_value": "1684431479.0000000",
-                                            "title": "Job Start Time",
-                                            "value": "2023-05-18 19:37:59"
-                                        },
-                                        {
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-                                            "plugin": "core",
-                                            "raw_value": "1684431577.0000000",
-                                            "title": "Job End Time",
-                                            "value": "2023-05-18 19:39:37"
-                                        },
-                                        {
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-                                            "plugin": "core",
-                                            "raw_value": "98.0000000",
-                                            "title": "Job Runtime (Wall Clock)",
-                                            "value": "1 minute"
-                                        },
-                                        {
-                                            "name": "cpuacct.usage",
-                                            "plugin": "cgroup",
-                                            "raw_value": "160336864240.0000000",
-                                            "title": "CPU Time",
-                                            "value": "2 minutes"
-                                        },
-                                        {
-                                            "name": "memory.failcnt",
-                                            "plugin": "cgroup",
-                                            "raw_value": "106968.0000000",
-                                            "title": "Failed to allocate memory count",
-                                            "value": 106968.0
-                                        },
-                                        {
-                                            "name": "memory.limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "4160749568.0000000",
-                                            "title": "Memory limit on cgroup (MEM)",
-                                            "value": "3.9 GB"
-                                        },
-                                        {
-                                            "name": "memory.max_usage_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "4160749568.0000000",
-                                            "title": "Max memory usage (MEM)",
-                                            "value": "3.9 GB"
-                                        },
-                                        {
-                                            "name": "memory.memsw.limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "9223372036854771712.0000000",
-                                            "title": "Memory limit on cgroup (MEM+SWP)",
-                                            "value": "8.0 EB"
-                                        },
-                                        {
-                                            "name": "memory.memsw.max_usage_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "4160880640.0000000",
-                                            "title": "Max memory usage (MEM+SWP)",
-                                            "value": "3.9 GB"
-                                        },
-                                        {
-                                            "name": "memory.oom_control.oom_kill_disable",
-                                            "plugin": "cgroup",
-                                            "raw_value": "1.0000000",
-                                            "title": "OOM Control enabled",
-                                            "value": "No"
-                                        },
-                                        {
-                                            "name": "memory.oom_control.under_oom",
-                                            "plugin": "cgroup",
-                                            "raw_value": "0E-7",
-                                            "title": "Was OOM Killer active?",
-                                            "value": "No"
-                                        },
-                                        {
-                                            "name": "memory.soft_limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "0E-7",
-                                            "title": "Memory softlimit on cgroup",
-                                            "value": "0 bytes"
-                                        }
-                                    ],
-                                    "job_stderr": "",
-                                    "job_stdout": "",
-                                    "model_class": "Job",
-                                    "output_collections": {},
-                                    "outputs": {
-                                        "outfile": {
-                                            "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                            "src": "hda",
-                                            "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                        }
-                                    },
-                                    "params": {
-                                        "__input_ext": "\"tabular\"",
-                                        "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                        "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                        "complement": "\"\"",
-                                        "count": "\"5\"",
-                                        "dbkey": "\"?\""
-                                    },
-                                    "state": "ok",
-                                    "stderr": "",
-                                    "stdout": "",
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-                                    "tool_stderr": "",
-                                    "tool_stdout": "",
-                                    "traceback": null,
-                                    "update_time": "2023-05-18T17:39:41.632086",
-                                    "user_email": "hxr@informatik.uni-freiburg.de"
-                                }
-                            ],
-                            "model_class": "WorkflowInvocationStep",
-                            "order_index": 5,
-                            "output_collections": {},
-                            "outputs": {
-                                "outfile": {
-                                    "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                    "src": "hda",
-                                    "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                }
-                            },
-                            "state": "scheduled",
-                            "subworkflow": null,
-                            "subworkflow_invocation_id": null,
-                            "update_time": "2023-05-18T17:39:41.615934",
-                            "workflow_step_id": "4c5e84542536cc7c",
-                            "workflow_step_label": null,
-                            "workflow_step_uuid": "820fd964-2460-4b50-8491-968d796500fc"
-                        },
-                        "6. Unnamed step": {
-                            "action": null,
-                            "id": "9869e0dcfb157198",
-                            "job_id": "11ac94870d0bb33a1d0bbfc0189b52a3",
-                            "jobs": [
-                                {
-                                    "command_line": "python /opt/galaxy/server/tools/filters/joinWrapper.py /data/dnb08/galaxy_db/files/c/f/b/dataset_cfb71055-95ff-4a95-9e0b-7a48161d5d0c.dat /data/dnb08/galaxy_db/files/2/8/2/dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat 4 1 N /data/jwd02f/main/060/036/60036244/outputs/galaxy_dataset_1c27a522-57c3-4dd6-a98b-2978def89473.dat",
-                                    "command_version": null,
-                                    "create_time": "2023-05-18T17:34:36.507964",
-                                    "dependencies": [],
-                                    "exit_code": 0,
-                                    "external_id": "43511832",
-                                    "galaxy_version": "23.0",
-                                    "history_id": "a7e26bbbb0830b20",
-                                    "id": "11ac94870d0bb33a1d0bbfc0189b52a3",
-                                    "inputs": {
-                                        "input1": {
-                                            "id": "4838ba20a6d86765828ccbcc3eb28a4b",
-                                            "src": "hda",
-                                            "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
-                                        },
-                                        "input2": {
-                                            "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                            "src": "hda",
-                                            "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                        }
-                                    },
-                                    "job_messages": [],
-                                    "job_metrics": [
-                                        {
-                                            "name": "hostname",
-                                            "plugin": "hostname",
-                                            "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
-                                            "title": "hostname",
-                                            "value": "vgcnbwc-worker-c36m100-0658.novalocal"
-                                        },
-                                        {
-                                            "name": "galaxy_slots",
-                                            "plugin": "core",
-                                            "raw_value": "1.0000000",
-                                            "title": "Cores Allocated",
-                                            "value": "1"
-                                        },
-                                        {
-                                            "name": "galaxy_memory_mb",
-                                            "plugin": "core",
-                                            "raw_value": "3891.0000000",
-                                            "title": "Memory Allocated (MB)",
-                                            "value": "3891"
-                                        },
-                                        {
-                                            "name": "start_epoch",
-                                            "plugin": "core",
-                                            "raw_value": "1684431607.0000000",
-                                            "title": "Job Start Time",
-                                            "value": "2023-05-18 19:40:07"
-                                        },
-                                        {
-                                            "name": "end_epoch",
-                                            "plugin": "core",
-                                            "raw_value": "1684431645.0000000",
-                                            "title": "Job End Time",
-                                            "value": "2023-05-18 19:40:45"
-                                        },
-                                        {
-                                            "name": "runtime_seconds",
-                                            "plugin": "core",
-                                            "raw_value": "38.0000000",
-                                            "title": "Job Runtime (Wall Clock)",
-                                            "value": "38 seconds"
-                                        },
-                                        {
-                                            "name": "cpuacct.usage",
-                                            "plugin": "cgroup",
-                                            "raw_value": "9278612295.0000000",
-                                            "title": "CPU Time",
-                                            "value": "9.278612295 seconds"
-                                        },
-                                        {
-                                            "name": "memory.failcnt",
-                                            "plugin": "cgroup",
-                                            "raw_value": "0E-7",
-                                            "title": "Failed to allocate memory count",
-                                            "value": 0.0
-                                        },
-                                        {
-                                            "name": "memory.limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "4160749568.0000000",
-                                            "title": "Memory limit on cgroup (MEM)",
-                                            "value": "3.9 GB"
-                                        },
-                                        {
-                                            "name": "memory.max_usage_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "191029248.0000000",
-                                            "title": "Max memory usage (MEM)",
-                                            "value": "182.2 MB"
-                                        },
-                                        {
-                                            "name": "memory.memsw.limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "4219351040.0000000",
-                                            "title": "Memory limit on cgroup (MEM+SWP)",
-                                            "value": "3.9 GB"
-                                        },
-                                        {
-                                            "name": "memory.memsw.max_usage_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "191029248.0000000",
-                                            "title": "Max memory usage (MEM+SWP)",
-                                            "value": "182.2 MB"
-                                        },
-                                        {
-                                            "name": "memory.oom_control.oom_kill_disable",
-                                            "plugin": "cgroup",
-                                            "raw_value": "1.0000000",
-                                            "title": "OOM Control enabled",
-                                            "value": "No"
-                                        },
-                                        {
-                                            "name": "memory.oom_control.under_oom",
-                                            "plugin": "cgroup",
-                                            "raw_value": "0E-7",
-                                            "title": "Was OOM Killer active?",
-                                            "value": "No"
-                                        },
-                                        {
-                                            "name": "memory.soft_limit_in_bytes",
-                                            "plugin": "cgroup",
-                                            "raw_value": "0E-7",
-                                            "title": "Memory softlimit on cgroup",
-                                            "value": "0 bytes"
-                                        }
-                                    ],
-                                    "job_stderr": "",
-                                    "job_stdout": "",
-                                    "model_class": "Job",
-                                    "output_collections": {},
-                                    "outputs": {
-                                        "out_file1": {
-                                            "id": "4838ba20a6d8676569e7a7744709f3b7",
-                                            "src": "hda",
-                                            "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
-                                        }
-                                    },
-                                    "params": {
-                                        "__input_ext": "\"bed\"",
-                                        "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                        "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                        "dbkey": "\"?\"",
-                                        "field1": "\"4\"",
-                                        "field2": "\"1\"",
-                                        "mode": "\"N\""
-                                    },
-                                    "state": "ok",
-                                    "stderr": "",
-                                    "stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
-                                    "tool_id": "comp1",
-                                    "tool_stderr": "",
-                                    "tool_stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
-                                    "traceback": null,
-                                    "update_time": "2023-05-18T17:40:47.707639",
-                                    "user_email": "hxr@informatik.uni-freiburg.de"
-                                }
-                            ],
-                            "model_class": "WorkflowInvocationStep",
-                            "order_index": 6,
-                            "output_collections": {},
-                            "outputs": {
-                                "out_file1": {
-                                    "id": "4838ba20a6d8676569e7a7744709f3b7",
-                                    "src": "hda",
-                                    "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
-                                }
-                            },
-                            "state": "scheduled",
-                            "subworkflow": null,
-                            "subworkflow_invocation_id": null,
-                            "update_time": "2023-05-18T17:40:47.686290",
-                            "workflow_step_id": "70e011a3c2da60d6",
-                            "workflow_step_label": null,
-                            "workflow_step_uuid": "52698c72-b6cc-4ca4-84b0-c84dd018e389"
-                        }
-                    }
-                },
-                "problem_log": "No log for this engine type.",
-                "start_datetime": "2023-05-18T19:32:20.395205",
-                "status": "success"
-            },
-            "doc": "Test sample data for the workflow",
-            "has_data": true,
-            "id": "galaxy-intro-101-workflow.ga_0",
-            "test_type": "galaxy_workflow"
-        }
-    ],
-    "version": "0.1"
-}
\ No newline at end of file
diff --git a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
index 36b781bae14c16..ef583a8c89af3d 100644
--- a/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
+++ b/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
@@ -12,11 +12,19 @@
             "class": "Person",
             "identifier": "0000-0001-9760-8992",
             "name": "Helena Rasche"
+        },
+        {
+            "class": "Person",
+            "identifier": "0000-0001-7649-2388",
+            "name": "Armin Dadras"
         }
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "name": "Find exons with the highest number of features",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
     "steps": {
         "0": {
             "annotation": "Input exons file",
@@ -34,8 +42,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 0,
-                "top": 187.2359999999986
+                "left": 1.39474626168904,
+                "top": 57.86883750870836
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"tag\": null}",
@@ -61,8 +69,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 49,
-                "top": 430.2359999999986
+                "left": 0,
+                "top": 214.13218366906176
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"tag\": null}",
@@ -74,7 +82,7 @@
         },
         "2": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0",
             "errors": null,
             "id": 2,
             "input_connections": {
@@ -88,10 +96,6 @@
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool bedtools Intersect intervals",
-                    "name": "inputA"
-                },
                 {
                     "description": "runtime parameter for tool bedtools Intersect intervals",
                     "name": "reduce_or_iterate"
@@ -106,19 +110,19 @@
                 }
             ],
             "position": {
-                "left": 323,
-                "top": 384.2359999999986
+                "left": 300,
+                "top": 144.13218366906176
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "a1a923cd89e8",
+                "changeset_revision": "2892111d91f8",
                 "name": "bedtools",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"bed\": false, \"count\": false, \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"header\": false, \"inputA\": {\"__class__\": \"RuntimeValue\"}, \"invert\": false, \"once\": false, \"overlap_mode\": [\"-wb\"], \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": {\"__class__\": \"RuntimeValue\"}}, \"sorted\": false, \"split\": false, \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.30.0+galaxy1",
+            "tool_state": "{\"bed\": false, \"count\": false, \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"genome_file_opts\": {\"genome_file_opts_selector\": \"loc\", \"__current_case__\": 0, \"genome\": null}, \"header\": false, \"inputA\": {\"__class__\": \"ConnectedValue\"}, \"invert\": false, \"once\": false, \"overlap_mode\": [\"-wb\"], \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": {\"__class__\": \"ConnectedValue\"}}, \"sorted\": false, \"split\": false, \"strand\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.31.1+galaxy0",
             "type": "tool",
             "uuid": "4fc2b17c-64d8-4c1c-a2d3-743f2ea9bcaf",
             "when": null,
@@ -126,7 +130,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -141,23 +145,23 @@
             "outputs": [
                 {
                     "name": "out_file",
-                    "type": "tabular"
+                    "type": "input"
                 }
             ],
             "position": {
-                "left": 618,
-                "top": 444.2359999999986
+                "left": 600,
+                "top": 144.13218366906176
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "562f3c677828",
+                "changeset_revision": "4c07ddedc198",
                 "name": "datamash_ops",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"grouping\": \"4\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"10\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.1.0",
+            "tool_state": "{\"grouping\": \"4\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"countunique\", \"op_column\": \"10\"}], \"print_full_line\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.8+galaxy0",
             "type": "tool",
             "uuid": "d6710e24-dbfb-4aef-8a63-2836cdc831e4",
             "when": null,
@@ -165,7 +169,7 @@
         },
         "4": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0",
             "errors": null,
             "id": 4,
             "input_connections": {
@@ -174,12 +178,7 @@
                     "output_name": "out_file"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Sort",
-                    "name": "infile"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Sort",
             "outputs": [
@@ -189,19 +188,19 @@
                 }
             ],
             "position": {
-                "left": 663.5,
-                "top": 0.0
+                "left": 900,
+                "top": 144.13218366906176
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "6073bb457ec0",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"RuntimeValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.1.1",
+            "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"n\"}], \"unique\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
             "uuid": "9311b83d-8ff6-4398-be37-9416281ccfac",
             "when": null,
@@ -209,7 +208,7 @@
         },
         "5": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0",
             "errors": null,
             "id": 5,
             "input_connections": {
@@ -228,19 +227,19 @@
                 }
             ],
             "position": {
-                "left": 896,
-                "top": 29.735999999998604
+                "left": 1200,
+                "top": 144.13218366906176
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "ddf54b12c295",
+                "changeset_revision": "6073bb457ec0",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"complement\": \"\", \"count\": \"5\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.1.0",
+            "tool_state": "{\"complement\": \"\", \"count\": \"5\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.5+galaxy0",
             "type": "tool",
             "uuid": "820fd964-2460-4b50-8491-968d796500fc",
             "when": null,
@@ -271,8 +270,8 @@
                 }
             ],
             "position": {
-                "left": 1133,
-                "top": 208.2359999999986
+                "left": 1466.5262322725052,
+                "top": 0.0
             },
             "post_job_actions": {
                 "RenameDatasetActionout_file1": {
@@ -301,6 +300,6 @@
     "tags": [
         "introduction"
     ],
-    "uuid": "274102ef-c8cf-47eb-933e-a1afd5b46891",
-    "version": 1
+    "uuid": "d924debe-dc54-4d60-b7e1-4f4e16ac44f5",
+    "version": 3
 }
\ No newline at end of file
diff --git a/topics/introduction/tutorials/galaxy-intro-101/workflows/test-data/top_5_exons.bed b/topics/introduction/tutorials/galaxy-intro-101/workflows/test-data/top_5_exons.bed
new file mode 100644
index 00000000000000..746c860e9c3f05
--- /dev/null
+++ b/topics/introduction/tutorials/galaxy-intro-101/workflows/test-data/top_5_exons.bed
@@ -0,0 +1,5 @@
+chr22	46256560	46263322	ENST00000253255.7_cds_0_0_chr22_46256561_r	0	-
+chr22	22514001	22515630	ENST00000302097.3_cds_0_0_chr22_22514002_r	0	-
+chr22	31712082	31717291	ENST00000327423.11_cds_5_0_chr22_31712083_r	0	-
+chr22	36191074	36191912	ENST00000352371.5_cds_0_0_chr22_36191075_r	0	-
+chr22	50546243	50549951	ENST00000648057.3_cds_0_0_chr22_50546244_f	0	+


Reviews:
user: login: bgruening
state: COMMENTED
author_association: MEMBER
submitted_at: 2025-04-11T11:07:06Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-11T11:28:45Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-11T11:28:49Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-11T11:29:08Z
user: login: teresa-m
body: Hi @dadrasarmin, sorry, after hosting the page locally, I saw some things that could be improved. It is mainly the size of the images. I am very sorry, this means a lot of work. But it would be great if you could zoom in before you take a screenshot. Or only take the image of the parts which is important. It is not easy to read the text in your screenshots. 
Secondly, there are some images in the linked FAQs that can be updated. But I would give this a low priority. Most of the time, one can still understand the image. We can put this on the ToDo list: 'if there is time left'. :)
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-15T14:51:48Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-15T15:53:58Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-15T15:54:15Z
user: login: bgruening
state: COMMENTED
author_association: MEMBER
submitted_at: 2025-04-21T18:31:15Z
user: login: bgruening
body: Just one comment.
state: DISMISSED
author_association: MEMBER
submitted_at: 2025-04-21T18:31:37Z
user: login: dadrasarmin
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T06:20:29Z

Review comments:
path: topics/introduction/images/101_bed_intersect_interface.png
user: login: bgruening
body: can we maybe not make this image to wide?
created_at: 2025-04-11T11:04:30Z
author_association: MEMBER
path: topics/introduction/images/configure_wf_output.png
user: login: bgruening
body: too many white space and maybe too large? the important stuff is too small?
created_at: 2025-04-11T11:05:44Z
author_association: MEMBER
diff_hunk: @@ -58,7 +60,19 @@ recordings:
   - natalie-wa
   bot-timestamp: 1726511277
 
-
+answer_histories:
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: bgruening
body: Nice, thanks!
created_at: 2025-04-11T11:06:00Z
author_association: MEMBER
path: topics/introduction/images/101_bed_intersect_interface.png
user: login: dadrasarmin
body: Is this better?
created_at: 2025-04-11T11:28:45Z
author_association: COLLABORATOR
path: topics/introduction/images/configure_wf_output.png
user: login: dadrasarmin
body: Is this better?
created_at: 2025-04-11T11:28:49Z
author_association: COLLABORATOR
diff_hunk: @@ -58,7 +60,19 @@ recordings:
   - natalie-wa
   bot-timestamp: 1726511277
 
-
+answer_histories:
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: dadrasarmin
body: Valar Dohaeris.
created_at: 2025-04-11T11:29:08Z
author_association: COLLABORATOR
path: topics/introduction/images/drag_n_drop_dataset.gif
user: login: teresa-m
body: Can you zoom in a bit? It is hard to read the text. Thanks a lot! 
created_at: 2025-04-15T14:18:00Z
author_association: COLLABORATOR
path: topics/introduction/images/histories_side_by_side_view.png
user: login: teresa-m
body: Can you zoom in a bit before making this screenshot? It is hard to read the text. Thanks a lot!
created_at: 2025-04-15T14:20:26Z
author_association: COLLABORATOR
path: topics/introduction/images/workflow_cards.png
user: login: teresa-m
body: Can you cut out the left-upper half of this screenshot? We don't need the Histories on the right and the notification bell on the bottom. Thanks
created_at: 2025-04-15T14:22:17Z
author_association: COLLABORATOR
path: topics/introduction/images/wf_editor_open.png
user: login: teresa-m
body: Again too small to read. Please zoom in. 
created_at: 2025-04-15T14:23:39Z
author_association: COLLABORATOR
path: topics/introduction/images/101_rename.png
user: login: teresa-m
body: Too small, please zoom in.
created_at: 2025-04-15T14:25:38Z
author_association: COLLABORATOR
path: topics/introduction/images/workflow_running.png
user: login: teresa-m
body: Too small. Please zoom in.
created_at: 2025-04-15T14:26:26Z
author_association: COLLABORATOR
diff_hunk: @@ -110,7 +124,7 @@ The Galaxy interface consists of three main parts:
 3. Your analysis **History** is recorded on the right
 
 
-![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.svg "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
+![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.png "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: teresa-m
body: The feature of turning the activity bar on and off is gone, as we only have the activity bar. 
If so we can remove the (Don't see ...) part and the Tip below ({% snippet faqs/galaxy/activity_bar_how_to_enable.md %})
If we should keep it the image in the FAQ needs to be updated.
created_at: 2025-04-15T14:29:52Z
author_association: COLLABORATOR
path: topics/introduction/images/101_datamash_1.png
user: login: teresa-m
body: Sorry, I am a bit picky. But again, it would be great if you could zoom in a bit. There is a lot of not used space in the middel. 
created_at: 2025-04-15T14:37:09Z
author_association: COLLABORATOR
diff_hunk: @@ -110,7 +124,7 @@ The Galaxy interface consists of three main parts:
 3. Your analysis **History** is recorded on the right
 
 
-![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.svg "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
+![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.png "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: teresa-m
body: Maybe not you, but in FAQ: {% snippet faqs/galaxy/histories_create_new.md %}, the screenshot also needs to be updated.
created_at: 2025-04-15T14:41:40Z
author_association: COLLABORATOR
diff_hunk: @@ -58,7 +60,19 @@ recordings:
   - natalie-wa
   bot-timestamp: 1726511277
 
-
+answer_histories:
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: teresa-m
body: Cool, I did not know about this feature! Thanks a lot for adding them. 
created_at: 2025-04-15T14:47:05Z
author_association: COLLABORATOR
path: topics/introduction/images/workflow_setting_inputs.png
user: login: teresa-m
body: Could you please increase?
created_at: 2025-04-15T14:47:37Z
author_association: COLLABORATOR
path: topics/introduction/images/configure_wf_output.png
user: login: teresa-m
body: Sorry, but a bit bigger would be great.
created_at: 2025-04-15T14:48:20Z
author_association: COLLABORATOR
path: topics/introduction/images/101_bed_intersect_interface.png
user: login: teresa-m
body: Still a bit bigger ,please. 
created_at: 2025-04-15T14:49:02Z
author_association: COLLABORATOR
diff_hunk: @@ -110,7 +124,7 @@ The Galaxy interface consists of three main parts:
 3. Your analysis **History** is recorded on the right
 
 
-![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.svg "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
+![Galaxy interface screenshot showing History panel on the right, tools panel on the left, and main panel in the center](../../images/galaxy_interface.png "<b>Galactic triptych</b>: the three panels of Galaxy interface: <em>Tools</em>, <em>Center Panel</em>, and <em>History</em>. Here you also see the 'Activity bar' that can be turned on and off (Don't see the Activity Bar? See a Tip below).")
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: dadrasarmin
body: These FAQs need to be updated:

- faqs/galaxy/account_create.md
- faqs/galaxy/activity_bar_how_to_enable.md
- faqs/galaxy/histories_create_new.md
- faqs/galaxy/datasets_change_dbkey.md
- faqs/galaxy/histories_list.md
- faqs/galaxy/histories_side_by_side_view.md
- faqs/galaxy/workflows_run.md
- faqs/galaxy/histories_sharing.md
- faqs/galaxy/datasets_change_datatype.md
- topics/contributing/tutorials/updating_tutorial/tutorial.html

 Unfortunately, I cannot invest more time on GTA2025 as updating tutorials. I have to write a report for ESG until end of April and I am behind the schedule there.
created_at: 2025-04-15T15:53:58Z
author_association: COLLABORATOR
path: topics/introduction/images/drag_n_drop_dataset.gif
user: login: dadrasarmin
body: I will update the photos.
created_at: 2025-04-15T15:54:15Z
author_association: COLLABORATOR
diff_hunk: @@ -478,7 +492,7 @@ You can create as many histories as you want. If you create a new history, your
 
 ![Overview of histories with their datasets](../../images/histories_side_by_side_view.png "Histories side-by-side view: in this view you drag datasets between histories, switch between histories, create new histories etc.")
 
-You can always return to your analysis view by clicking on Home icon {% icon galaxy-home %} (**Analyze Data** on older versions of Galaxy) in the top menu bar.
+You can always return to your analysis view by clicking on Galaxy name Icon in the top menu bar.
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: bgruening
body: Maybe just `Galaxy name` or just `Galaxy icon`?
created_at: 2025-04-21T18:31:15Z
author_association: MEMBER
diff_hunk: @@ -478,7 +492,7 @@ You can create as many histories as you want. If you create a new history, your
 
 ![Overview of histories with their datasets](../../images/histories_side_by_side_view.png "Histories side-by-side view: in this view you drag datasets between histories, switch between histories, create new histories etc.")
 
-You can always return to your analysis view by clicking on Home icon {% icon galaxy-home %} (**Analyze Data** on older versions of Galaxy) in the top menu bar.
+You can always return to your analysis view by clicking on Galaxy name Icon in the top menu bar.
path: topics/introduction/tutorials/galaxy-intro-101/tutorial.md
user: login: dadrasarmin
body: Done.
created_at: 2025-04-22T06:20:29Z
author_association: COLLABORATOR

PR comments:
user: login: dadrasarmin
created_at: 2025-04-11T11:28:19Z
body: I updated [the FAQ for `gtn_workflow_testing`](https://training.galaxyproject.org/training-material/faqs/gtn/gtn_workflow_testing.html) because it has a typo. It says the test file should end with `test.yaml` which is not correct and should be `tests.yaml`. We can see the correct pattern in multiple merged tutorials.
author_association: COLLABORATOR
user: login: teresa-m
created_at: 2025-04-15T10:26:22Z
body: @dadrasarmin: Thanks a lot. to me, the changes look all good. I am not an expert on the workflows. @Delphine-L or  @shiltemann, could you have a look at these files?
author_association: COLLABORATOR
user: login: teresa-m
created_at: 2025-04-16T09:48:59Z
body: @dadrasarmin: Thanks a lot for your changes! From my side, the tutorial is good to go. Could someone please have a look at the workflows? 
author_association: COLLABORATOR
user: login: bgruening
created_at: 2025-04-22T06:35:04Z
body: Thanks!

author_association: MEMBER