Merge pull request #1140 from mvdbeek/fix_genotype_aware_variant_calling_workflow

Fix genotype aware variant calling workflow

Author: mvdbeek

scripts/workflow_manifest.py

@@ -67,7 +67,7 @@ def get_dockstore_details(trsID):
         else:
             print("No 'id' field found in the top-level data.")
     else:
-        print(f"Failed to retrieve details. Status code: {response.status_code}")
+        print(f"Failed to retrieve details for {trsID} from {url_details}. Status code: {response.status_code}")
     return details, categories, collections
 
 

workflows/variant-calling/ploidy-aware-genotype-calling/.dockstore.yml

@@ -3,9 +3,9 @@ workflows:
 - name: main
   subclass: Galaxy
   publish: true
-  primaryDescriptorPath: /generic-genotype+variant-calling-wgs-pe.ga
+  primaryDescriptorPath: /genotype-variant-calling-wgs-pe.ga
   testParameterFiles:
-  - /generic-genotype+variant-calling-wgs-pe-test.yml
+  - /genotype-variant-calling-wgs-pe-test.yml
   authors:
   - name: Saim Momin
     orcid: 0009-0003-9935-828X

workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.1.1] 2026-03-12
+
+- Rename workflow file to remove '+' character from filename.
+
 ## [0.1] 2026-02-18
 
 First release.

…genotype+variant-calling-wgs-pe-test.yml …genotype-variant-calling-wgs-pe-test.ymlworkflows/variant-calling/ploidy-aware-genotype-calling/generic-genotype+variant-calling-wgs-pe-test.yml renamed to workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml workflows/variant-calling/ploidy-aware-genotype-calling/generic-genotype+variant-calling-wgs-pe-test.yml renamed to workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml

@@ -86,7 +86,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1",
+    "release": "0.1.1",
     "name": "Paired end variant and ploidy-aware genotype calling",
     "readme": "This workflow performs end-to-end germline variant and genotype calling on paired-end Illumina sequencing data from organisms of any given ploidy. Starting from raw FASTQ reads, the workflow handles quality control, read mapping, duplicate removal, variant and genotype calling with FreeBayes, and functional annotation of the resulting variants.",
     "report": {