nf-core / nf-core/variantprioritization
Param `--pcgr_run_arguments` instead of divided params?
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- Dominant language
- Nextflow
- Stars
- 16
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Instead of organizing your input argumetns like this in nextflow.config
tumor_site = 10
...
to something like this
pcgr_preparevcf_options = "--tumor_site 10 ..."
It allows the user more flexibility (without having to make a completely new config) in sacrifice of some variable interpretability.
Some examples:
https://github.com/search?q=org%3Anf-core+path%3Anextflow.config+_options+OR+arguments_+&type=code
Originally posted by @Joon-Klaps in https://github.com/nf-core/variantprioritization/pull/64#discussion_r2938954284
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 nextflow.config and the existing parameter definitions for tumor_site and related PCGR inputs. Compare them with the _options or arguments patterns linked in the issue, then trace where these parameters are consumed. Done means agreeing on and applying a consistent configuration interface without requiring a separate config for each combination of inputs.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, tooling
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100