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Correctly skip nested subworkflows #1019

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Merged
GlassOfWhiskey merged 1 commit into from
Apr 11, 2026
+19 −10
Merged

Correctly skip nested subworkflows #1019

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8 changes: 4 additions & 4 deletions .github/workflows/ci-tests.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,24 +40,24 @@ jobs:
- commit: "76bdf9b55e2378432e0e6380ccedebb4a94ce483"
exclude: "docker_entrypoint,modify_file_content"
version: "v1.2"
- commit: "6eddbfb03b8861885832b26e322fbd0fcb9a884d"
- commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
exclude: "docker_entrypoint,modify_file_content"
version: "v1.3"
- docker: "singularity"
commit: "6eddbfb03b8861885832b26e322fbd0fcb9a884d"
commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
exclude: "docker_entrypoint,modify_file_content,iwd-container-entryname1"
on: "ubuntu-24.04"
python: "3.14"
version: "v1.3"
- docker: "kubernetes"
commit: "6eddbfb03b8861885832b26e322fbd0fcb9a884d"
commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
exclude: "docker_entrypoint,modify_file_content"
on: "ubuntu-24.04"
python: "3.14"
version: "v1.3"
- on: "macos-15-intel"
python: "3.14"
commit: "6eddbfb03b8861885832b26e322fbd0fcb9a884d"
commit: "e71ddcc925d64c2efa68c2a56dd0edcc960a2170"
exclude: "docker_entrypoint,modify_file_content"
version: "v1.3"
runs-on: ${{ matrix.on }}
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21 changes: 15 additions & 6 deletions streamflow/cwl/translator.py
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Expand Up @@ -2919,17 +2919,26 @@ def _translate_workflow_step(
port_name, combinator_step.get_input_port(port_name)
)
# Add skip ports if there is a condition without a loop
if cwl_condition and loop is None:
elif cwl_condition:
for element_output in cwl_element.out:
global_name = utils.get_name(step_name, cwl_step_name, element_output)
port_name = posixpath.relpath(global_name, step_name)
skip_port = (
external_output_ports[global_name]
if loop is not None
else internal_output_ports[global_name]
# Create cond forwarder to avoid propagating SKIPPED tokens
# within a subworkflow
cond_forwarder = workflow.create_step(
cls=ForwardTransformer,
name=global_name + "-output-forward-transformer",
)
cond_forwarder.add_output_port(
port_name, internal_output_ports[global_name]
)
internal_output_ports[global_name] = workflow.create_port()
cond_forwarder.add_input_port(
port_name, internal_output_ports[global_name]
)
# Point the skip port to the output port of the forwarder
cast(CWLConditionalStep, conditional_step).add_skip_port(
port_name, skip_port
port_name, cond_forwarder.get_output_port()
)
# Update output ports with the internal ones
self.output_ports |= internal_output_ports
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