Is there any way to specify the alignment output should be in cram format?

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

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Is there any way to specify the alignment output should be in cram format? #220

Open vulpescu opened 2 years ago

vulpescu commented 2 years ago

This feature could free up terabytes of storage on large projects, but it looks like pepatac is hard-coded to use bam format. Are there any plans to add an "output to cram" flag?