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smaht-dac · Nov 29, 2023 · b847737 · b847737
1 parent 88c44b8
commit b847737
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/pipeline_utils/lib/yaml_parser.py b/pipeline_utils/lib/yaml_parser.py
@@ -390,6 +390,11 @@ def _arguments(self, input, consortia):
                         for i, name_ in enumerate(v):
                             v_.append({self.FILE_SCHEMA: f'{self._string_consortia(consortia)}:{self.REFERENCEFILE_TYPE_SCHEMA}-{name_.replace("@", "_")}',
                                        self.DIMENSION_SCHEMA: str(i)})
+                        # remove DIMENSION_SCHEMA field if only one file
+                        #   this is necessary so the file will be posted as a string and not a list
+                        #   having a list will break tibanna creating the correct input for cwltool
+                        if len(v_) == 1:
+                            del v_[0][self.DIMENSION_SCHEMA]
                         argument_.setdefault(k, v_)
                     elif k == self.QC_THRESHOLDS_SCHEMA:
                         v_ = {