Typed CWL parsers

Author: GlassOfWhiskey

cwl_utils/cite_extract.py

@@ -33,7 +33,7 @@ def main() -> int:
 
 
 def extract_software_reqs(
-    process: cwl.Process,
+    process: cwl.Process | cwl.WorkflowStep,
 ) -> Iterator[cwl.SoftwareRequirement]:
     """Return an iterator over any SoftwareRequirements found in the given process."""
     if process.requirements:

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -1465,6 +1465,7 @@ def traverse_CommandLineTool(
                         inp.linkMerge = None
                     for index, out in enumerate(new_clt_step.out):
                         new_clt_step.out[index] = out.split("/")[-1]
+
                     for tool_inp in new_clt_step.run.inputs:
                         tool_inp.id = tool_inp.id.split("#")[-1]
                     for tool_out in new_clt_step.run.outputs:

cwl_utils/docker_extract.py

@@ -102,7 +102,9 @@ def extract_docker_requirements(
         yield req
 
 
-def extract_docker_reqs(process: cwl.Process) -> Iterator[cwl.DockerRequirement]:
+def extract_docker_reqs(
+    process: cwl.Process | cwl.WorkflowStep,
+) -> Iterator[cwl.DockerRequirement]:
     """For the given process, extract the DockerRequirement(s)."""
     if process.requirements:
         for req in process.requirements: