I'm experiencing a disk usage warning using Toil with CWL:

w01.cbio.private 2018-10-17 04:22:20,803 Thread-403 WARNING toil.statsAndLogging: Got message from job at time 10-17-2018 04:22:20: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job 3/1/jobrLeFLD/g/tmp53AwFF.tmp used 119.21% (234.0 GB [251278385152B] used, 196.3 GB [210788941824B] requested) at the end of its run.
w01.cbio.private 2018-10-17 04:22:20,823 Thread-403 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_0.0.40/ACCESS-Pipeline/cwl_tools/umi_qc/make_umi_qc_tables.cwl' make_umi_qc_tables.sh q/z/jobq8gG4P    WARNING:toil.fileStore:LOG-TO-MASTER: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job 3/1/jobrLeFLD/g/tmp53AwFF.tmp used 119.21% (234.0 GB [251278385152B] used, 196.3 GB [210788941824B] requested) at the end of its run.

However, the outputs from this step are less than 1MB.

With Toil with CWL, do the input files count towards the outdirMax limit?

Or is there another source that contributes to this limit?

Thank you!