Mutect CWL Tool

Simple CWL wrapper for mutect-1.1.7 for use with TinDaisy. Based on OpenGenomics/mutect-tool

For development and testing purposes, this project ships with test data and demonstration scripts for running directly (in docker container), by calling docker image, and by calling CWL tool. See ./testing for details.

Docker image: "dinglab2/mutect-tool:20200427"

Memory issues

Jobs which die suddenly with "Killed" error output may be caused by running out of memory.

There are three parameters to tweak in a cromwell run:

• Java parameter Xmx?g, maximum memory in g per job
• rammin - parameter passed to cromwell to request memory for container
• ncpu - number of jobs running at once

The hypothesis is that NCPU * Xmx <= RamMin, on the thinking that each thread requires Xmx and there will be NCPU of them, so at least RamMin must be provided

Setting Xmx2g, rammin = 18, ncpu = 8 seems to be stable.

Contact: Matt Wyczalkowski (m.wyczalkowski@wustl.edu)