nf-core pipelines with unpinned nf-validation plugin
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template
WIP
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
| Name | in dev |
in last release |
|---|---|---|
| nf-core/airrflow | ❌ | ❌ |
| nf-core/atacseq | ✅ | ❌ |
| nf-core/bacass | ✅ | ❌ |
| nf-core/bamtofastq | ✅ | ❌ |
| nf-core/crisprseq | ✅ | ❌ |
| nf-core/differentialabundance | ✅ | ❌ |
| nf-core/funcscan | ✅ | ❌ |
| nf-core/hicar | ❌ | ❌ |
| nf-core/isoseq | ❌ | ❌ |
| nf-core/marsseq | ❌ | ❌ |
| nf-core/metaboigniter | ✅ | ❌ |
| nf-core/metapep | ❌ | |
| nf-core/mhcquant | ✅ | ❌ |
| nf-core/quantms | ❌ | ❌ |
| nf-core/raredisease | ✅ | ❌ |
| nf-core/riboseq | ✅ | |
| nf-core/rnafusion | ✅ | ❌ |
| nf-core/sammyseq | ❌ | ❌ |
| nf-core/sarek | ✅ | ❌ |
| nf-core/viralintegration | ❌ | ❌ |
based on the following query: gh api "/search/code?q=org:nf-core%20'nf-validation'%20filename:nextflow.config" --jq '.items[].repository.full_name' | sort
Contributor 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.
Research direction
Start with the listed nf-core repositories and their nextflow.config files; the issue includes a gh api search command to identify configurations containing nf-validation. Review the affected pipelines and determine the expected pinned plugin version before updating them, then rerun the search to confirm the unpinned configurations are resolved.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100