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update test to new upstream subworkflow structure #4038

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Merged
mashehu merged 2 commits into from
Feb 11, 2026
Merged

update test to new upstream subworkflow structure #4038

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update test to new upstream subworkflow structure
mashehu Feb 11, 2026
d31dedd
[automated] Update CHANGELOG.md
nf-core-bot Feb 11, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,8 @@

### Subworkflows

- update test to new upstream subworkflow structure ([#4038](https://github.com/nf-core/tools/pull/4038))

### Pipeline template

#### Version updates
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3 changes: 0 additions & 3 deletions tests/subworkflows/test_update.py
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Expand Up @@ -366,9 +366,6 @@ def test_update_change_of_included_modules(self):
# Check that tabix/bgziptabix is not there
assert "tabix/bgziptabix" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir()
# Check that tabix/tabix is there
assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir()
# Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming)
assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]
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