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Update GRCh38 reference #35
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Description
Goal:
Update GRCh38 reference test data file
Context:
The repository contains a GRCh38 reference in the test data, but it is unclear how the reference was generated and if it's the latest version.
Files/components to update:
resources_test_scripts/reference_tiny.sh: Add code to generate a subsampled GRCh38 reference. Ideally this reference would be a subsampled version of the latest GRCh38 referenceresources_test/GRCh38: Update the referencesrc/mapping/spaceranger_count: validate that tests work with this updated reference. In principle, spaceranger also accepts a .tar.gz reference format. If possible, include a test for both the .tar.gz reference and the uncompressed reference.
Resources:
- See https://www.10xgenomics.com/support/software/space-ranger/downloads for latest version
- See https://github.com/openpipelines-bio/openpipeline/blob/main/resources_test_scripts/ref_gencodev41_chr1.sh for subsampling reference
- See https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/custom-references for more info on generating references
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