Skip to content
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

Linting error if quay.io found in biocontainer name #2278

Merged
merged 8 commits into from
May 9, 2023
Merged

Linting error if quay.io found in biocontainer name #2278

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
4bad234
error if quay.io found in docker container name
adamrtalbot May 4, 2023
aea396a
More verbose error explanation
ewels May 5, 2023
86aee0c
Add passed test if quay.io is correct
adamrtalbot May 5, 2023
4351a34
Container status check only occurs once
adamrtalbot May 5, 2023
27fb44a
Merge branch 'dev' into catch_modules_with_quay.io
adamrtalbot May 9, 2023
46c1dea
Checks for any instance of quay.io in container name
adamrtalbot May 9, 2023
c786f2a
Improved log message
adamrtalbot May 9, 2023
00bd8ef
update gitlab sha
mirpedrol May 9, 2023
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 @@ -7,6 +7,7 @@
### Linting

- Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))
- Error if module container specification has quay.io as prefix when it shouldn't have.

### Modules

Expand Down
8 changes: 8 additions & 0 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 @@ -290,6 +290,14 @@ def check_process_section(self, lines, fix_version, progress_bar):
else:
self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
docker_tag = None
if l.startswith("quay.io/biocontainers") and not l.startswith("quay.io/biocontainers/mulled"):
self.failed.append(
(
"container_links",
"quay.io/biocontainers prefix found, please use biocontainers instead",
ewels marked this conversation as resolved.
Show resolved Hide resolved
self.main_nf,
)
)
if l.startswith("biocontainers/"):
# When we think it is a biocontainer, assume we are querying quay.io/biocontainers and insert quay.io as prefix
l = "quay.io/" + l
Expand Down