Whats our stance on the

save_output_as_bam

parameter. Because for parabricks it writes out

cram

files. Thats a little misleading then. However also converting them to bam seems to be just extra compute time. Same goes for writing directly to bam. Its not supported by parabricks to have both bam and cram as outputs. So we either have to convert the parabricks-crams to bam to give them to the user or we need to convert parabricks-bams to crams to continue the workflow.