Skip to content

fix failing pytest for lint after samtools topic conversion #4026

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mashehu wants to merge 3 commits into
base: dev
Choose a base branch
from
+6 −2
Open

fix failing pytest for lint after samtools topic conversion #4026

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
323fdb0
fix failing pytest for lint after samtools topic conversion
mashehu Feb 2, 2026
33cb5e8
[automated] Update CHANGELOG.md
nf-core-bot Feb 2, 2026
9542f29
add todo reminder
Feb 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@

### Linting

- fix failing pytest for lint after samtools topic conversion ([#4026](https://github.com/nf-core/tools/pull/4026))

### Modules

### Subworkflows
Expand Down
6 changes: 4 additions & 2 deletions tests/subworkflows/test_lint.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -504,7 +504,8 @@ def test_lint_clean_patch(self):

assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
assert len(subworkflow_lint.passed) > 0
assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
# TODO: Add count test back, once we have finished topic conversion
# assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
assert any(
[
x.message.endswith("Can be ignored if the module is using topic channels")
Expand All @@ -528,7 +529,8 @@ def test_lint_broken_patch(self):
errors = [x.message for x in subworkflow_lint.failed]
assert "Subworkflow patch cannot be cleanly applied" in errors
assert len(subworkflow_lint.passed) > 0
assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
# TODO: Add count test back, once we have finished topic conversion
# assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
assert any(
[
x.message.endswith("Can be ignored if the module is using topic channels")
Expand Down
Loading