Port OpenMS TOPP tools to nf-core
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Description
Following discussion in Slack, several local modules introduced in nf-core/mhcquant#447 are generically useful for proteomics workflows and belong upstream in nf-core/modules alongside other tools in their respective suites (notably the broader OpenMS suite). Initially tracked here nf-core/mhcquant#296, now better visible on nf-core/modules repo.
Scope
- Port the OpenMS-related local modules currently living in nf-core/mhcquant to nf-core/modules so they can be reused by other proteomics pipelines. They just need to be ported
- Port further OpenMS TOPP tools to nf-core
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 by reviewing the local OpenMS-related modules referenced in nf-core/mhcquant#447 and comparing them with the corresponding tool modules in nf-core/modules. Define which additional OpenMS TOPP tools are in scope, then port the agreed modules and validate them using the repository’s module and nf-test conventions; done means the reusable modules are available upstream for other proteomics workflows.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100