Simplifying output structure to reflect the change of multiome pipeli…

…ne's output name to secondary_analysis.h5mu

bin/azimuth/write_metadata.py

@@ -89,10 +89,6 @@ def main(orig_secondary_analysis_matrix:Path, secondary_analysis_h5ad: Path, ver
     else:
         ad.write("secondary_analysis.h5ad")  # save final secondary analysis matrix
 
-    #Both outputs are optional now, throw an error if neither is written out so that the CWL workflow returns failure
-    if not orig_secondary_analysis_matrix.name.exists() and not Path("secondary_analysis.h5ad").exists():
-        raise ValueError(f"Neither {orig_secondary_analysis_matrix.name} nor secondary_analysis.h5ad written")
-
 
 if __name__ == "__main__":
     p = ArgumentParser()

pipeline-manifest.json

@@ -1,12 +1,7 @@
 [
 	{
-		"pattern": "secondary_analysis\\.h5ad",
+		"pattern": "secondary_analysis\\.*",
 		"description": "Normalized gene expression with additional metadata, in HDF5 format, readable with the 'anndata' Python package",
 		"edam_ontology_term": "EDAM_1.24.format_3590"
-	},
-	{
-		"pattern": "multiome_normalized\\.h5mu",
-		"description": "Normalized gene expression and chromatin accessibility with additional metadata, in HDF5 format, readable with the 'muon' Python package",
-		"edam_ontology_term": "EDAM_1.24.format_3590"
 	}
 ]

pipeline.cwl

@@ -64,4 +64,4 @@ steps:
       version_metadata:
         source: azimuth/version_metadata
     out:
-      - annotated_matrix
+      - annotated_matrix

steps/write-metadata.cwl

@@ -29,8 +29,4 @@ outputs:
   annotated_matrix:
     type: File?
     outputBinding:
-      glob: "secondary_analysis.h5ad"
-  annotated_multiome_matrix:
-    type: File?
-    outputBinding:
-      glob: "multiome_normalized.h5ad"
+      glob: "secondary_analysis*"