STAR command is not using TMP dir - moving and removing files created in the outputdir

[slsevilla]

Problem

RENEE STAR is removing and moving files from the output directory as it processes, which makes it difficult to debug errors.

RENEE/workflow/rules/paired-end.smk

Line 375 in 3975071

# SAMtools sort (uses less memory than STAR SortedByCoordinate)

Solution

Output should be put in TEMP and final files should be moved to final output/dir location. This will also allow Snakemake to cleanup any files created when there is an error