galaxyproject / galaxyproject/iwc

RNAseq PE: coverage calculation step fails workflow when no reads are aligned

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Description

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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

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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.

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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

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