nf-core / nf-core/test-datasets
Clean up bam/cram homo_sapiens files for modules tests data
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Description
Bam and Cram files did (partially) not use the same reference fasta for generating them. It is not clear by name which used which and defeats the purpose of having mapped, duplicatemarked,recalibrated bam/cram files all based on the same original dataset. This probably happened when we faced repeated issues with the then existing files not having enough coverage for some variant calling tools. I think it should be cleaned up and replaced though.
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Research direction
Start by inventorying the BAM and CRAM files used as module test data and the reference FASTA associated with each. Trace which files were generated from the same original dataset, then replace inconsistent files so the mapped, duplicate-marked, and recalibrated data share one reference and provide sufficient coverage for variant-calling tests.
Written by the indexing model from the issue text.
Assessment
- Domain
- testing
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100