temp dir standardization (low priority)

[tyamaguchi-ucla]

Yeah, we'll have to remove the temp_dir from the config.. I thought we already did but that was for Spark.. I just created a new issue.

So, here it looks like the temp_dir is used for the pipeline workDir as well as the temp dir of Picard (since we generally use temp_dir=/scratch). We'll need to standardize how we handle tool temp directories and pipeline workDir.

For now, I think we can just resolve #181 and release the major version as discussed to minimize the chance of breaking the cluster...

In the long run, we may want to have a specific temp dir for each process/tool as default to make the temp/workDir dir structure cleaner, debugging easier, and avoid potential temp dir conflicts (probably unlikely but just in case).

As default, maybe we can do something like

/scratch/${pipeline-name}-${runName}/tmp/${process_name} (tool name should be in the process name)
/scratch/align-DNA-${runName}/tmp/run-MarkDuplicatesSpark-GATK
/scratch/align-DNA-${runName}/workDir

We can discuss this next week.

Originally posted by @tyamaguchi-ucla in #180 (comment)