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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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New docker image for cellranger 6.0.0 #56

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

This PR addresses #55 which requires addition of a new docker image for cellranger 6.0.0 to be used for benchmarking pre-processing of ScPCA data.

The old dockerfile used for cellranger 4.0.0 was moved to a new file named cellranger4.docker and the new Dockerfile contains the image for running cellranger 6.0.0. The docker image was built and tested using the following command: docker run -it --rm scpca-cellranger:6.0.0 cellranger testrun --id=tiny to ensure that it successfully can run cellranger 6.0.0.

Additionally, it appears that the reference files for cellranger have not been updated since July 7, 2020 and the reference files located on S3 were added in October, 2020. The STARsolo website also doesn't mention any need for a new reference index. I think it is safe to assume that we do not need to update the reference. https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest

Things that have not been done:

jashapiro commented 3 years ago

Actually... I realized that there is one more step that needs to be done... updating images/cellranger/README.md to reflect the changes. You can either do that in this PR as well before merging, or in a separate PR.