nf-core / nf-core/deepmodeloptim
[enhancement] do .yaml config parsing and puting into channels in groovy instead of python
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 31
- Forks
- 14
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
currently .yaml config parsing/splitting into multiple yamls happens in a python process, we would like this to happen in groovy for multiple reasons :
- python programs do not use .yaml files, this is specific to the nextflow pipeline
- would not require stimlus-py container to split .yaml files
- more in line with nf-core/nextflow philosophy
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
Locate the current Python process that parses and splits .yaml files, then find where the Nextflow pipeline puts the resulting files into channels. The work is done when equivalent parsing and splitting happens in Groovy without requiring the stimlus-py container.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 28/100