ensure cwl files are absolute

viash-hub · Aug 9, 2024 · cbbc222 · cbbc222
1 parent 94f9fc6
commit cbbc222
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/bd_rhapsody/bd_rhapsody_make_reference/script.py b/src/bd_rhapsody/bd_rhapsody_make_reference/script.py
@@ -110,7 +110,7 @@ def get_cwl_file(meta: dict[str, Any]) -> str:
     # create cwl file (if need be)
     cwl_file=os.path.join(meta["resources_dir"], "make_rhap_reference_2.2.1_nodocker.cwl")
 
-    return cwl_file
+    return os.path.abspath(cwl_file)
 
 def main(par: dict[str, Any], meta: dict[str, Any]):
     config = read_config(meta["config"])

diff --git a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/script.py b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/script.py
@@ -156,7 +156,7 @@ def generate_cwl_file(meta: dict[str, Any], dir: str) -> str:
     else:
         cwl_file = orig_cwl_file
 
-    return cwl_file
+    return os.path.abspath(cwl_file)
 
 def copy_outputs(par: dict[str, Any], config: dict[str, Any]):
     for arg in config["arguments"]: