Hi everyone, thanks for the great work on this pipeline. I’d like to perform somatic variant calling with GATK Mutect2 using the BAM files after Base Quality Score Recalibration. However, it seems that these recalibrated BAM files are not saved among the final outputs of the pipeline. Is there currently a way to either: Save the recalibrated BAMs produced after ApplyBQSR, or Access them from within the workflow (e.g., via a specific channel or parameter), so they can be reused for downstream analyses such as Mutect2? Thanks a lot for your help!

I haven't used this pipeline myself -- I would have guessed the recalibrated BAMs should get saved, sinc they are the "final" BAMs, right? What does

--save_align_intermeds

do? If there is no way to save the recalibrated BAMs, then that's definitely a bug.