Merge branch 'galaxyproject:main' into add_wf_annotation_maker

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,6 +5,7 @@ FOR CONTRIBUTOR:
 
 FOR REVIEWERS:
 * [ ] .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
+* [ ] Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
 * [ ] In workflow: annotation field contains short description of what the workflow does. Should start with `This workflow does/runs/performs … xyz … to generate/analyze/etc …`
 * [ ] In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
 * [ ] In workflow: `name` field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-workflow-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_24.0
+  GALAXY_BRANCH: release_24.1
   MAX_CHUNKS: 40
 jobs:
   setup:

.github/workflows/workflow_test.yml

@@ -22,7 +22,7 @@ jobs:
       python-version-list: "[\"3.11\"]"
       max-chunks: 4
       galaxy-fork: galaxyproject
-      galaxy-branch: release_24.0
+      galaxy-branch: release_24.1
 
   # Planemo lint the changed repositories
   lint:
@@ -69,7 +69,7 @@ jobs:
       python-version-list: "[\"3.11\"]"
       repository-list: ${{ needs.setup.outputs.repository-list }}
       galaxy-fork: galaxyproject
-      galaxy-branch: release_24.0
+      galaxy-branch: release_24.1
       check-outputs: false
 
   combine_outputs:

.gitignore

@@ -3,3 +3,4 @@ tool_test_output.json
 .DS_Store
 workflow_manifest.json
 .vscode
+*_diagrams.md

README.md

@@ -34,7 +34,7 @@ All IWC workflows are automatically installed onto usegalaxy.* servers (i.e. [Ga
 
 ## Contributing a Workflow
 
-Anyone can contribute a Galaxy Workflow. Please check out the [Adding workflow guidelines](workflows/README.md#adding-workflows).
+Anyone can contribute a production Galaxy Workflow. Please check out the [Adding workflow guidelines](workflows/README.md#adding-workflows).
 
 If linting passes, tests pass, and human review passes, the PR is merged and
 

workflows/README.md

@@ -19,6 +19,17 @@ The structure is as follows:
 
 ## Adding workflows
 
+### Workflow eligibility
+
+We want to collect production workflows targeted at users that want to analyze their own data.
+As such, the workflow should be sufficiently generic that users can provide their own data.
+
+We encourage, but do not require, links to related [Galaxy Training Network Tutorials](https://training.galaxyproject.org/).
+Importantly, each workflow should be described in a way that a user can run the
+workflow on their own data without modifying the workflow. If you wish to
+deposit a workflow that accompanies a tutorial please make sure that the workflow
+does not refer to datasets that only make sense in the context of the tutorial.
+
 Here are some guidelines to help new contributors to add their workflows.
 
 Everything starts from a workflow that you have on a galaxy instance.

workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.4] 2024-12-16
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1`
+
 ## [0.3] 2024-11-11
 
 ### Automatic update

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## [0.1.9] 2024-12-17
+### Added
+- Annotation for workflow describing its function
 
 ## [0.1.8] 2024-12-03
 

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml

@@ -29,16 +29,16 @@
       delta: 10000
     GenomeScope summary:
       asserts:
-        has_text:
-            text: '27,842 bp'
-        has_text:
-            text: '35,913 bp'
+        - has_text_matching:
+            expression: '27,84. bp'
+        - has_text_matching:
+            expression: '35,91. bp'
     GenomeScope Model Parameters:
       asserts:
-        has_text:
-            text: '0.0918418396430493'
-        has_text:
-            text: '27.44263'
+        - has_text_matching:
+            expression: '0.09184.*'
+        - has_text_matching:
+            expression: '27.44.*'
     Merged Meryl Database:
       asserts:
         has_size:

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "",
+    "annotation": "Performs k-mer profiling on PacBio data and generates GenomeScope plots and summary for genome characteristics assessment.",
     "comments": [],
     "creator": [
         {
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.1.8",
+    "release": "0.1.9",
     "name": "kmer-profiling-hifi-VGP1",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"