Error when running skipper in paired end mode
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- Dominant language
- Python
- Stars
- 10
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
When running Skipper in paired-end (PE) mode, Snakemake fails during job preparation with a permission error because the workflow tries to create/use a TSCC-specific temp path under /tscc. This appears to be caused by a hard-coded tmpdir value in skipper/rules/basic/pe_preprocess.smk.
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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 at skipper/rules/basic/pe_preprocess.smk around line 136 and inspect the hard-coded tmpdir used by the paired-end workflow. Reproduce or review Snakemake job preparation in PE mode, then verify the workflow no longer attempts to create or use the TSCC-specific /tscc path and completes preparation with an accessible temporary location.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 55/100