Merge pull request galaxyproject#4092 from wm75/sars-surveillance-update

Update the SARS-CoV-2 variant discovery tutorial

faqs/galaxy/datasets_import_from_data_library.md

@@ -9,11 +9,17 @@ contributors: [bebatut,shiltemann,nsoranzo,hexylena,wm75]
 
 As an alternative to uploading the data from a URL or your computer, the files may also have been made available from a *shared data library*:
 
-* Go into **Shared data** (top panel) then **Data libraries**
-* Navigate to
-{% if include.path %}
-  *{{ include.path }}* or {% endif %} the correct folder as indicated by your instructor
-* Select the desired files
-* Click on the **To History** button near the top and select **{{ include.astype | default: "as Datasets" }}** from the dropdown menu
-* In the pop-up window, select the history you want to import the files to (or create a new one)
-* Click on **Import**
+1. Go into **Shared data** (top panel) then **Data libraries**
+2. Navigate to{% if include.path %}: *{{ include.path }}* or {% endif %} the correct folder as indicated by your instructor
+3. Select the desired files
+4. Click on **Add to History** {% icon galaxy-dropdown %} near the top and select **{{ include.astype | default: "as Datasets" }}** from the dropdown menu
+5. In the pop-up window, choose
+   {% if include.collection_type %}
+   * *"Collection type"*: **{{ include.collection_type }}**
+   {% endif %}
+   * *"Select history"*: {% if include.tohistory %}{{ include.tohistory }}{% else %}the history you want to import the data to (or create a new one){% endif %}
+6. Click on {% if include.collection_type %}**Continue**{% else %}**Import**{% endif %}
+{% if include.collection_type %}
+7. In the next dialog, give a suitable **Name**{% if include.collection_name %}, like `{{ include.collection_name }}`,{% endif %} to the new collection
+8. Click on **Create collection**
+{% endif %}

faqs/galaxy/workflows_import_search.md

@@ -3,27 +3,17 @@ title: Importing a workflow using the search
 area: workflows
 box_type: tip
 layout: faq
-contributors: [bebatut]
+contributors: [bebatut,wm75]
 ---
 
-- Click on *Workflow* on the top menu bar of Galaxy. You will see a list of all your workflows.
-- Click on the {% icon galaxy-upload %} **Import** icon at the top-right of the screen
-- Click on **search form** in **Import a Workflow from Configured GA4GH Tool Registry Servers (e.g. Dockstore)**
-{% if include.trs_server %}
-- Select *"TRS Server"*: `{{ include.trs_server }}`
-{% else %}
-- Select the relevant TRS Server
-{% endif %}
-{% if include.search_query %}
-- Type `{{ include.search_query }}` in the search query
-{% else %}
-- Type the query
-{% endif %}
-{% if include.workflow_name %}
-- Expand the workflow named `{{ include.workflow_name }}`
-{% else %}
-- Expand the correct workflow
-{% endif %}
-- Click on the wanted version
+1. Click on *Workflow* in the top menu bar of Galaxy. You will see a list of all your workflows.
+2. Click on the {% icon galaxy-upload %} **Import** icon at the top-right of the screen
+3. On the new page, select the **GA4GH servers** tab, and configure the **GA4GH Tool Registry Server (TRS) Workflow Search** interface as follows:
+   1. *"TRS Server"*: {% if include.trs_server %}**{{ include.trs_server }}**{% else %}the TRS Server you want to search on (Dockstore or Workflowhub){% endif %}
+   2. {% if include.search_query %}*"search query"*: `{{ include.search_query }}`
+      {% else %}Type in the *search query*{% endif %}
+   3. {% if include.workflow_name %}Expand the workflow named `{{ include.workflow_name }}`
+      {% else %}Expand the correct workflow{% endif %} by clicking on it
+   4. Select the version you would like to {% icon galaxy-upload %} import
 
-    The workflow will be imported in your workflows
+The workflow will be imported to your list of workflows. Note that it will also carry a little green check mark next to its name, which indicates that this is an original workflow version imported from a TRS server. If you ever modify the workflow with Galaxy's workflow editor, it will lose this indicator.