Rearrange processes to output BAM at the end

[yashpatel6]

Currently, the recalibrated BAM is an output of a process that is intermediate in the pipeline. We'd like to re-arrange this to have the BAM, index, and checksums be output at the end of the workflow to ensure that when those files are ready to be output, there aren't any other dependent processes that may have issues if the files are moved instead of copied