Parabricks modules need `stageInMode 'copy'`
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Description
Have you checked the docs?
Description of the bug
See this thread on the slack: https://nfcore.slack.com/archives/C04SDJYV12L/p1731421258620959
For now it's going to be a requirement that they all be in the same folder. But I'm talking to the engineering team about if it's possible to change that in a future release.
If parabricks gets updated - check whether the stageInMode 'copy' can be removed.
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 Parabricks modules and the linked Slack thread, then check whether the relevant Parabricks release still requires all inputs in one folder. No file or test is named; done means confirming whether stageInMode 'copy' can be removed and updating the affected modules if the requirement has changed.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100