Thanks to visit codestin.com
Credit goes to github.com

Skip to content

fix ternary container linting #3830

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

Merged
merged 2 commits into from
Oct 15, 2025
Merged

fix ternary container linting #3830

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
10bd3bc
remove ternary operators from container lines
mashehu Oct 15, 2025
245bbdc
[automated] Update CHANGELOG.md
nf-core-bot Oct 15, 2025
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
- Use the org from .nf-core.yml when linting multiqc_config report_comment ([#3800](https://github.com/nf-core/tools/pull/3800))
- Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
- Add link to modules and subworkflows linting error docs ([#3818](https://github.com/nf-core/tools/pull/3818))
- fix ternary container linting ([#3830](https://github.com/nf-core/tools/pull/3830))

### Modules

Expand Down
6 changes: 3 additions & 3 deletions nf_core/modules/lint/main_nf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -314,11 +314,11 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
# Deprecated enable_conda
for i, raw_line in enumerate(lines):
url = None
line = raw_line.strip(" \n'\"}:")
line = raw_line.strip(" \n'\"}:?")

# Catch preceding "container "
if line.startswith("container"):
line = line.replace("container", "").strip(" \n'\"}:")
line = line.replace("container", "").strip(" \n'\"}:?")

if _container_type(line) == "conda":
if "bioconda::" in line:
Expand Down Expand Up @@ -592,7 +592,7 @@ def check_process_labels(self, lines):
def check_container_link_line(self, raw_line, registry):
"""Look for common problems in the container name / URL, for docker and singularity."""

line = raw_line.strip(" \n'\"}:")
line = raw_line.strip(" \n'\"}:?")

# lint double quotes
if line.count('"') > 2:
Expand Down
9 changes: 9 additions & 0 deletions tests/modules/lint/test_main_nf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,15 @@ def test_process_labels(content, passed, warned, failed):
0,
1,
),
# Ternary with ? on next line (new Nextflow format) should pass
(
'''container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data'
: 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264'}"''',
6,
0,
0,
),
],
)
def test_container_links(content, passed, warned, failed):
Expand Down