Merge branch 'main' into fc-dorado-workflow-standalone-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
@@ -287,4 +292,9 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /workflows/utilities/wf_dorado_basecalling.wdl
    testParameterFiles:
-    - /tests/inputs/empty.json
+    - /tests/inputs/empty.json
+ - name: Concatenate_Illumina_Lanes_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/file_handling/wf_concatenate_illumina_lanes.wdl
+   testParameterFiles:
+     - /tests/inputs/empty.json

.github/PULL_REQUEST_TEMPLATE.md

@@ -45,7 +45,8 @@ This PR uses an element that could cause duplicate runs to have different result
 - [ ] The workflow/task has been tested and results, including file contents, are as anticipated
 - [ ] The CI/CD has been adjusted and tests are passing (Theiagen developers)
 - [ ] Code changes follow the [style guide](https://theiagen.notion.site/Style-Guide-WDL-Workflow-Development-51b66a47dde54c798f35d673fff80249)
-- [ ] Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)
+- [ ] Documentation and/or workflow diagrams have been updated if applicable
+  - [ ] You have updated the latest version for any affected worklows in the respective workflow documentation page and for every entry in the three `workflows_overview` tables.
 
 ## 🎯 Reviewer Checklist
 <!--  Indicate NA when not applicable  -->

README.md

@@ -42,30 +42,32 @@ 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
-* **James Otieno** ([@jrotieno](https://github.com/jrotieno)) - 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
 * **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
 
 ### External Contributors
 
 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)) 
 * **Robert Petit** ([@rpetit3](https://github.com/rpetit3))
+* **Emma Doughty** ([@emmadoughty](https://github.com/emmadoughty))
 * **Ash O'Farrel** ([@aofarrel](https://github.com/aofarrel))
 * **Sam Baird** ([@sam-baird](https://github.com/sam-baird))
 * **Holly Halstead** ([@HNHalstead](https://github.com/HNHalstead))
+* **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1))
 
 ### Maintaining PHB Pipelines
 

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