galaxyproject / galaxyproject/iwc
RNAseq PE: coverage calculation step fails workflow when no reads are aligned
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Description
This seems rather unfortunate for large projects. Should we do `$0~"Uniquely mapped reads number"{print 1000000/($NF+1)}` instead in the `get scaling factor step` ? ping @lldelisle
Contributor guide
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Research direction
Start by locating the RNAseq PE workflow's “get scaling factor step” and inspect how it handles samples with no aligned reads. Reproduce the failure with an input producing zero aligned reads, then verify that the workflow completes and produces a valid scaling-factor result for that case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- awk
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100