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Subworkflow lint bugfixes #3968

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Subworkflow lint bugfixes #3968

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13d425b
If a line is empty/comment, this needs to be checked before changing …
andresferben Dec 10, 2025
2f4733d
In case more than one subworkflow is defined in the same file
andresferben Dec 10, 2025
3bcc2b9
[automated] Update CHANGELOG.md
nf-core-bot Dec 10, 2025
301c3c5
Update changelog
andresferben Dec 10, 2025
52f582d
Merge branch 'dev' of https://github.com/andresferben/tools into dev
andresferben Dec 10, 2025
0c00af9
Remove duplicated entries in changelog
andresferben Dec 10, 2025
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7 changes: 4 additions & 3 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,15 @@

### General

- dockerhub action: add disk clean-up step and combine the two actions ([#3926](https://github.com/nf-core/tools/pull/3926))
- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
- Switch from pre-commit to prek for pre-commit hooks in development([#3899](https://github.com/nf-core/tools/pull/3899))
- Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
- switch to uv and pyproject.toml ([#3925](https://github.com/nf-core/tools/pull/3925))
- dockerhub action: add disk clean-up step and combine the two actions ([#3926](https://github.com/nf-core/tools/pull/3926))
- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
- Pin j178/prek-action action to 91fd7d7 ([#3931](https://github.com/nf-core/tools/pull/3931))
- add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a ([#3946](https://github.com/nf-core/tools/pull/3946))
- Fix quote handling in meta.yml ([#3948](https://github.com/nf-core/tools/pull/3948))
- Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
- Update actions/checkout digest to 8e8c483 ([#3956](https://github.com/nf-core/tools/pull/3956))
- Update GitHub Actions ([#3957](https://github.com/nf-core/tools/pull/3957))
- Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
Expand All @@ -23,6 +23,7 @@
### Linting

- fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
- Fix bugs in subworkflows lint causing false positive warnings ([#3968](https://github.com/nf-core/tools/pull/3968))

### Modules

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8 changes: 4 additions & 4 deletions nf_core/subworkflows/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,15 +51,15 @@ def main_nf(_, subworkflow: NFCoreComponent) -> tuple[list[str], list[str]]:
workflow_lines = []
main_lines = []
for line in lines:
if re.search(r"^\s*workflow\s*\w*\s*{", line) and state == "subworkflow":
if not _is_empty(line) and re.search(r"^\s*workflow\s*\w*\s*{", line) and state in ["subworkflow", "emit"]:
state = "workflow"
if re.search(r"take\s*:", line) and state in ["workflow"]:
if not _is_empty(line) and re.search(r"take\s*:", line) and state in ["workflow"]:
state = "take"
continue
if re.search(r"main\s*:", line) and state in ["take", "workflow"]:
if not _is_empty(line) and re.search(r"main\s*:", line) and state in ["take", "workflow"]:
state = "main"
continue
if re.search(r"emit\s*:", line) and state in ["take", "main", "workflow"]:
if not _is_empty(line) and re.search(r"emit\s*:", line) and state in ["take", "main", "workflow"]:
state = "emit"
continue

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