nf-core / nf-core/genomeassembler
issues with genomescope2 module
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Description
Description of the bug
When attempting to switch to nf-core/genomescope to as part of #171, genomescope2 failed to converge for the full_test dataset.
The currently local genomescope module (genomescope.R in bin/) works fine and converges. The reasons for this are unclear, but may be worth figuring out.
Command used and terminal output
Relevant files
No response
System information
No response
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
Compare the nf-core/genomescope2 module with the local bin/genomescope.R implementation, using the full_test dataset and the context from issue #171. Reproduce the failure and investigate why genomescope2 does not converge; done means the full_test run converges successfully or the incompatibility is documented with evidence.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100