Small nits in pipeline template 4.2.1
Maintainers usually reply within 1 day
Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 68/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Active
- Tech stack
- github-actions, python
- Domain
- build-system, tooling
Research direction
Start by locating the pipeline template files awsfulltest.yml, nextflow.config, .github/workflows/nf-test.yml, and the block-pipeline-outdir pre-commit hook script. Compare the nf-schema versions and upload-artifact comments, then check how the hook handles filenames. Done when the three listed inconsistencies are resolved in the template.
Written by the indexing model from the issue text.
Description
Description of the bug
Found a handful of small nits when migrating over.
-
awsfulltest.ymlandnextflow.configdeclare different nf-schema versions -
block-pipeline-outdirpre-commit hook ignores the files it is given. Suggested fix: setpass_filenames: falseon the hook, or have the script iterate over"$@". - Inconsistent version comment on
upload-artifact..github/workflows/nf-test.ymlpinsactions/upload-artifactwith the comment# v7, while every other template workflow labels the same SHA# v7.0.2.
Command used and terminal output
`nf-core pipelines sync # nf-core/tools 4.2.1`
System information
- nf-core/tools 4.2.1
- Nextflow 25.10.4 and 26.10.4
- Pipeline: nf-core/fastquorum (
TEMPLATEbranch at the 4.2.1 sync commit)
- Dominant language
- Python
- Stars
- 327
- Forks
- 266
- Avg merge
- 1d 23h
- Merged PRs (30d)
- 33
Getting set up
Starts the project's dev container in your browser, under your own GitHub account.
- Ships a Dockerfile or Docker Compose file
- Has a pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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