nf-core / nf-core/variantbenchmarking
igv-reports
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- 31
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- 1d 22h
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Description
Description of feature
variant screenshots might be useful using IGV REPORT tool. The tool exist in nf-core modules yet it needs further implementation since it lacks --tracks parameter which is needed to add bam files.
one danger in adding this too is overheating the memory with many screenshots for the analysis including thousands of variants. Thus definitely will need a limit parameter,
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 existing IGV REPORT implementation in the nf-core modules and nf-core/modules PR #5263, especially the missing --tracks support. Then inspect how this pipeline invokes the tool. Done means variant screenshots can include BAM tracks and a limit prevents producing an unsafe number of screenshots.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100