Compare scratch usage between MarkDuplicatesSpark and SAMtools markdup

[tyamaguchi-ucla]

          @nkwang24 @yashpatel6 For multi-library samples, this approach would help although it will take some time to implement it. Also, it would be helpful to understand the usage of `/scratch` space between `MarkDuplicatesSpark` and `SAMtools markdup`.

Originally posted by @tyamaguchi-ucla in #234 (comment)

[tyamaguchi-ucla]

@yashpatel6 @j2salmingo I suggest that we work on this task before implementing #234 as it's relatively straightforward and it will provide important insights on /scratch usage. Also, unrelated but we might want to create a new release soon after we update the default reference path (alt-aware reference) in the template config.

[j2salmingo]

Just to keep everything in my head straight, let me know if there is something I am missing:

-Benchmark MarkDuplicatesSpark vs SAMTools markdup
-This can be done by isolating the process and creating one step pipelines for each one
-/scratch space can be measured by running some script that periodically runs du until the process finishes

Which BAM files should I be using for the benchmarking?
Was there a third option I forgot about?