nf-core update all depencencies (modules + subworkflows)
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
Right now when I want to update all modules and subworkflows in a pipeline, I do (ok, the -f might be too much)
nf-core modules update -afy ; nf-core subworkflows update -afy
But it feels un-efficient, as the first command will only update modules and depending subworkflows, and the second only subworkflows and depending modules.
I would love a single comment to update all dependencies
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 tracing the CLI entry points for nf-core modules update and nf-core subworkflows update, including how each command handles dependent components. The work is done when one command or option updates all modules and subworkflows without requiring both existing commands separately; add or update CLI tests if the relevant test locations are found.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100