(WIP) update most packages used

UCSF-DSCOLAB / data_processing_pipelines

A repository to store the existing pipelines to process the various CoLabs datasets

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Closed dtm2451 closed 2 years ago

dtm2451 commented 3 years ago

Not ready yet.

Major bits still to go:

[ ] use cram for picard steps now that we can
[ ] update STAR version and STAR/RSEM indexes to use a current Gencode transcriptome
[ ] update rRNA mapping method

arkal commented 2 years ago

@erflynn has verified this is good. Merging