nf-core / nf-core/tools

Handle deprecated and deleted modules/subworkflows gracefully

Open
#4,260 0 comments 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

enhancement
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description of feature

If a module/subworkflow is deprecated, we add a failure assertion in the file.
We are now discussing deleting the module/subworkflow entirely after a year or so.
These modules may still bepresent in the modules.json (and pipeline), we need to handle this.
Tools should handle this nicely.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing how modules.json and pipeline entries are handled when a module or subworkflow has been deprecated or deleted. Define the expected behavior for these remaining references, then verify that the tools handle them without an unhelpful failure.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
38/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.