updated h5ad with gs:// path for reference_gtf_file

pipelines/skylab/atac/atac.wdl

@@ -602,7 +602,19 @@ task CreateFragmentFile {
     # Add nhash_id to h5ad file as unstructured metadata
     atac_data.uns['NHashID'] = atac_nhash_id
 
-    atac_data.uns['GTF'] = str(atac_gtf)
+    # Add GTF to uns field
+    
+    # Original path from args.annotation_file
+    annotation_gtf = str(atac_gtf)  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+
+    # Transform the path
+    if annotation_gtf.startswith('/cromwell_root/'):
+        stripped_path = annotation_gtf[len('/cromwell_root/'):]  # Remove '/cromwell_root/'
+        updated_path = f'gs://{stripped_path}'  # Add 'gs://' prefix
+    else:
+        updated_path = str(atac_gtf)
+    
+    atac_data.uns["reference_gtf_file"] = updated_path
     # calculate tsse metrics
     snap.metrics.tsse(atac_data, atac_gtf)
     # Write new atac file