Converts a BAM into a SAM file. You need to specify a reference genome in FASTA format. The reference genome can be gz compressed.
This repo doesn’t contain any ref files due to their size; you’ll need to already have them.
dockstore workflow launch --local-entry bam_to_cram.wdl --json local.json
When using on Terra, use either gcs.json or gcs_downsample.json
This is a companion discussion topic for the original entry at github.com/aofarrel/BAM-to-CRAM-WDL