Merge pull request #6516 from katherine-d21/patch-2

Enhance tutorial with peptide annotation and queries

Author: subinamehta

faqs/galaxy/workflows_run.md

@@ -3,18 +3,19 @@ title: Running a workflow
 area: workflows
 box_type: tip
 layout: faq
-contributors: [shiltemann,hexylena,wm75, Marie59]
+contributors: [shiltemann,hexylena,wm75, Marie59,katherine-d21]
 ---
 
-1. Click on **Workflows** on the vertical panel on the left of the **Galaxy action list**  
-2. At the top of the resulting page you will have the option to switch between the *My workflows*, *Workflows shared with me* and *Public workflows* tabs. Select the tab {% if include.tab %}`{{ include.tab }}`{% else %} you want to see all workflows in that category.{% endif %}. 
-3. Search for {% if include.name %}`{{ include.name }}`{% else %} your desired workflow {% endif %}.
+1. Click on **Workflows** on the vertical panel on the left of the **Galaxy action list**.
+2. At the top of the resulting page you will have the option to switch between the *My workflows*, *Workflows shared with me* and *Public workflows* tabs.
+3. {% if include.tab %}Select the tab `{{ include.tab }}`{% else %}Select the tab you want to see all workflows in that category{% endif %}
+4. {% if include.name %}Search workflows `{{ include.name }}`{% else %}Search for your desired workflow{% endif %}.
 
 ![Select workflow]({% link topics/climate/images/bgc_calib/bgc_workflow.png %}){:width="15%"}
 
-4. Click on the workflow name: a pop-up window opens with a preview of the workflow  
-5. To run it directly: click **Run** (top-right)  
+5. Click on the workflow name: a pop-up window opens with a preview of the workflow.
+6. To run it directly: click **Run** (top-right).
 
-6. **Recommended**: click **Import** (left of Run) to make your own local copy under *Workflows / My Workflows*    
+7. **Recommended**: click **Import** (left of Run) to make your own local copy under *Workflows / My Workflows*.
 
 You may have to refresh your history to see the queued jobs

topics/proteomics/images/neoantigen/pvac.PNG

@@ -319,10 +319,8 @@ To rerun this entire analysis at once, you can use our workflow. Below we show h
 
 > <hands-on-title>Running the Workflow</hands-on-title>
 >
-> 1. **Import the workflow** into Galaxy:
->
->    {% snippet faqs/galaxy/workflows_run_trs.md path="topics/proteomics/tutorials/neoantigen-fragpipe-discovery/workflows/main_workflow.ga" title="Fragpipe Discovery" %}
->
+>  1. **Import the workflow** into Galaxy:
+>    - (Neoantigen Database Search)[https://tinyurl.com/ipepgen-dbsearch-wf]
 >
 > 2. Run **Workflow** {% icon workflow %} using the following parameters:
 >    - *"Send results to a new history"*: `No`
@@ -333,6 +331,13 @@ To rerun this entire analysis at once, you can use our workflow. Below we show h
 >
 >    {% snippet faqs/galaxy/workflows_run.md %}
 >
+> <comment-title>DISCLAIMER</comment-title>
+>
+> - If any step in this workflow fails, please ensure that the input files have been correctly generated and formatted by the preceding tools. Workflow failures often result from improperly called or incomplete input data rather than errors in the workflow itself. Users are responsible for verifying their input before troubleshooting workflow issues.
+>
+> {: .comment}
+>
+>
 {: .hands_on}
 
 # Are you feeling adventurous? ✨

topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.md

@@ -3,4 +3,5 @@ layout: workflow-list
 
 redirect_from:
   - /topics/proteomics/tutorials/neoantigen-3-fragpipe-discovery/workflows/
+  - /topics/proteomics/tutorials/neoantigen-fragpipe-discovery/workflows/main_workflow.html
 ---

topics/proteomics/tutorials/neoantigen-fragpipe-discovery/workflows/index.md

@@ -346,6 +346,7 @@ Using regex (regular expressions) for find and replace is a powerful technique f
 >    {% snippet faqs/galaxy/analysis_regular_expressions.md %}
 >
 > 2. Rename the output FASTA as `Arriba-Fusion-Database.fasta`
+> 
 {: .hands_on}
 
 
@@ -360,8 +361,7 @@ To rerun this entire analysis at once, you can use our workflow. Below, we show
 > <hands-on-title>Running the Workflow</hands-on-title>
 >
 > 1. **Import the workflow** into Galaxy:
->
->    {% snippet faqs/galaxy/workflows_run_trs.md path="topics/proteomics/tutorials/neoantigen-fusion-database-generation/workflows/main_workflow.ga" title="Neoantigen Fusion Database Generation" %}
+>    - (Neoantigen Fusion Database Generation)[https://tinyurl.com/ipepgen-gene-fusion-wf]
 >
 >
 > 2. Run **Workflow** {% icon workflow %} using the following parameters:
@@ -373,6 +373,12 @@ To rerun this entire analysis at once, you can use our workflow. Below, we show
 >
 >    {% snippet faqs/galaxy/workflows_run.md %}
 >
+> <comment-title>DISCLAIMER</comment-title>
+>
+> - If any step in this workflow fails, please ensure that the input files have been correctly generated and formatted by the preceding tools. Workflow failures often result from improperly called or incomplete input data rather than errors in the workflow itself. Users are responsible for verifying their input before troubleshooting workflow issues.
+>
+> {: .comment}
+>
 {: .hands_on}
 
 # Are you feeling adventurous? ✨

topics/proteomics/tutorials/neoantigen-fragpipe-discovery/workflows/main_workflow.ga

@@ -3,4 +3,5 @@ layout: workflow-list
 
 redirect_from:
   - /topics/proteomics/tutorials/neoantigen-1-fusion-database-generation/workflows/
+  - /topics/proteomics/tutorials/neoantigen-fusion-database-generation/workflows/main_workflow.html
 ---