Merge branch 'main' into smw-theiameta-panel-dev

.dockstore.yml

@@ -195,6 +195,11 @@ workflows:
    primaryDescriptorPath: /workflows/utilities/data_import/wf_terra_2_bq.wdl
    testParameterFiles:
     - /tests/inputs/empty.json
+ - name: Fetch_SRR_Accession_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/data_import/wf_fetch_srr_accession.wdl
+   testParameterFiles:
+    - /tests/inputs/empty.json
  - name: Concatenate_Column_Content_PHB
    subclass: WDL
    primaryDescriptorPath: /workflows/utilities/file_handling/wf_concatenate_column.wdl

README.md

@@ -42,19 +42,18 @@ You can expect a careful review of every PR and feedback as needed before mergin
 
 ### Authorship
 
-(Ordered by contribution [# of lines changed] as of 2024-08-01)
+(Ordered by contribution [# of lines changed] as of 2024-12-04)
 
 * **Sage Wright** ([@sage-wright](https://github.com/sage-wright)) - Conceptualization, Software, Validation, Supervision
 * **Inês Mendes** ([@cimendes](https://github.com/cimendes)) - Software, Validation
 * **Curtis Kapsak** ([@kapsakcj](https://github.com/kapsakcj)) - Conceptualization, Software, Validation
 * **Frank Ambrosio** ([@frankambrosio3](https://github.com/frankambrosio3)) - Conceptualization, Software, Validation
 * **Michelle Scribner** ([@michellescribner](https://github.com/michellescribner)) - Software, Validation
 * **Kevin Libuit** ([@kevinlibuit](https://github.com/kevinlibuit)) - Conceptualization, Project Administration, Software, Validation, Supervision
-* **Emma Doughty** ([@emmadoughty](https://github.com/emmadoughty)) - Software, Validation
 * **Fraser Combe** ([@fraser-combe](https://github.com/fraser-combe)) - Software, Validation
+* **Andrew Page** ([@andrewjpage](https://github.com/andrewjpage)) - Project Administration, Software, Supervision
 * **Michal Babinski** ([@Michal-Babins](https://github.com/Michal-Babins)) - Software, Validation
 * **Andrew Lang** ([@AndrewLangVt](https://github.com/AndrewLangVt)) - Software, Supervision
-* **Andrew Page** ([@andrewjpage](https://github.com/andrewjpage)) - Project Administration, Software, Supervision
 * **Kelsey Kropp** ([@kelseykropp](https://github.com/kelseykropp)) - Validation
 * **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1)) - Validation
 * **Joel Sevinsky** ([@sevinsky](https://github.com/sevinsky)) - Conceptualization, Project Administration, Supervision
@@ -63,7 +62,7 @@ You can expect a careful review of every PR and feedback as needed before mergin
 
 We would like to gratefully acknowledge the following individuals from the public health community for their contributions to the PHB repository:
 
-* **James Otieno** ([@jrotieno](https://github.com/jrotieno))
+* **James Otieno** ([@jrotieno](https://github.com/jrotieno)) 
 * **Robert Petit** ([@rpetit3](https://github.com/rpetit3))
 * **Emma Doughty** ([@emmadoughty](https://github.com/emmadoughty))
 * **Ash O'Farrel** ([@aofarrel](https://github.com/aofarrel))

docs/assets/new_workflow_template.md

@@ -4,14 +4,16 @@
 
 | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
 |---|---|---|---|---|
-| [Workflow Type](../../workflows_overview/workflows_type.md/#link-to-workflow-type) | [Applicable Kingdom](../../workflows_overview/workflows_kingdom.md/#link-to-applicable-kingdom) | PHB <version with last changes> | <command-line compatibility> | <workflow level on terra> |
+| [Link to Workflow Type](../../workflows_overview/workflows_type.md/#link-to-workflow-type) | [Link to Applicable Kingdom](../../workflows_overview/workflows_kingdom.md/#link-to-applicable-kingdom) | PHB <version with last changes\> | <command-line compatibility\> | <workflow level on terra (set or sample)\> |
 
 ## Workflow_Name_On_Terra
 
 Description of the workflow.
 
 ### Inputs
 
+Input should be ordered as they appear on Terra
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | task_name | **variable_name** | Type | Description | Default Value | Required/Optional |
@@ -24,12 +26,12 @@ Description of the workflow tasks
     Description of the task
 
     !!! techdetails "Tool Name Technical Details"
-        |  | Links | 
-        | --- | --- | 
+        |  | Links |
+        | --- | --- |
         | Task | [link to task on GitHub] |
         | Software Source Code | [link to tool's source code] |
         | Software Documentation | [link to tool's documentation] |
-        | Original Publication | [link to tool's publication] |
+        | Original Publication(s) | [link to tool's publication] |
 
 ### Outputs