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Support for sub workflows #103

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Support for sub workflows #103

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6558c1b
Support for subworkflows
manabuishii Sep 29, 2021
8a130c9
Fix missing global
manabuishii Sep 29, 2021
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7 changes: 5 additions & 2 deletions cwl_utils/docker_extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
)

ProcessType = Union[cwl.Workflow, cwl.CommandLineTool, cwl.ExpressionTool]

WorkflowDir = ""

def parse_args() -> argparse.Namespace:
"""Argument parser."""
Expand All @@ -34,9 +34,11 @@ def parse_args() -> argparse.Namespace:

def main(args: argparse.Namespace) -> None:
"""Extract the docker reqs and download them using Singularity or docker."""
global WorkflowDir
os.makedirs(args.dir, exist_ok=True)

top = cwl.load_document(args.input)
WorkflowDir = str(Path(args.input).parent)+"/"

for req in traverse(top):
if not req.dockerPull:
Expand Down Expand Up @@ -85,8 +87,9 @@ def traverse(process: ProcessType) -> Iterator[cwl.DockerRequirement]:

def get_process_from_step(step: cwl.WorkflowStep) -> ProcessType:
"""Return the process for this step, loading it if necessary."""
global WorkflowDir
if isinstance(step.run, str):
return cast(ProcessType, cwl.load_document(step.run))
return cast(ProcessType, cwl.load_document(WorkflowDir+step.run))
return cast(ProcessType, step.run)


Expand Down