nf-core / nf-core/modules

Linting fails for module with Dockerfile

Open
#7,781 4 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug
Dominant language
Nextflow
Stars
429
Forks
1.1k
Avg merge
1d 6h
Merged PRs (30d)
153

Description

Have you checked the docs?
Description of the bug

The spacerangermodule contains its own Dockerfile, as the Space Ranger software is not available in Biocontainers. When recently updating this Dockerfile with the latest version of Space Ranger, the linting of the module fails during CI with GitHub Actions; see https://github.com/nf-core/modules/pull/7233 for the relevant PR and https://nfcore.slack.com/archives/CJRH30T6V/p1740644857195529 for discussions on Slack.

This is sort of an edge case: not many modules have to have its own Dockerfile, and that Dockerfile is likely not often updated. Either the relevant Action would need to be updated to handle cases like this, or we somebody with admin privileges should ignore the failed linting and merge anyway.

Command used and terminal output
See linting on the PR (link above).
Relevant files

No response

System information

GitHub Actions.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linting run on PR 7233 and inspect the repository's GitHub Actions configuration for how modules containing a Dockerfile are handled. Determine whether the linting workflow can support the spaceranger case; done means the module passes CI linting without requiring an administrative bypass.

Written by the indexing model from the issue text.

Assessment

Tech stack
dockerfile, github-actions
Domain
ci-cd, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.