Here are a few things we've improved in RSEM for our RNA-Seq pipeline.
use move instead of system(mv...) as it works across filesystems
use a temporary directory with auto cleanup for storing intermediary files, which is very friendly for HPC systems storing temporary results in scratch
export STAR Log.final.out to the final directory
fix incorrect examples in rsem-calculate-expression docs
I'm not expecting everything here will be retained, especially the shared memory option for STAR. I can reintroduce the two removed parameters to adjust the temporary dir location and conditionally set CLEANUP.
Here are a few things we've improved in RSEM for our RNA-Seq pipeline.
moveinstead ofsystem(mv...)as it works across filesystemsLog.final.outto the final directoryI'm not expecting everything here will be retained, especially the shared memory option for STAR. I can reintroduce the two removed parameters to adjust the temporary dir location and conditionally set
CLEANUP.