Additional information for users of the nci-lp-dragen partition

The nci-lp-dragen partition as of June 2023 includes one dragen server configured to run the TSO500 ctDNA pipeline. It has been funded by NCI/CCR/Lab of Pathology until 30-Sep-2026.


Running a TSO500 ctDNA batch job
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Create a batch script similar to the following:

#! /bin/bash
# this is

# set up paths etc
source /etc/profile.d/

ANALYSIS="/staging/${RUNFOLDER}-ctDNA-$(date +%s)"

# clean up after run
trap 'rm -rf "/staging/${RUNFOLDER}" "${ANALYSIS}"' EXIT

cp -r "${RUNPATH}/${RUNFOLDER}" /staging || exit 100
mkdir -p "${ANALYSIS}" || exit 101

# may need to specify --sampleSheet if not in the default location --analysisFolder "${ANALYSIS}" \
    --runFolder "/staging/${RUNFOLDER}" \
2>&1 | tee "${ANALYSIS}/test.out" || exit 102

[[ -f "${METRICS}" ]] || printf "Missing metrics file\n"

# copy results back to working directory
cp -r "${ANALYSIS}" "${RESULTPATH}" || exit 103

And submit with

[user@biowulf]$ sbatch --mem=0 --cpus-per-task=64 --partition nci-lp-dragen --qos=compass

if you have access to the compass QOS which increases priority and max. walltime. Users without access to the QOS are limited to 8h max walltime.

Note that the $ANALYSIS folder is lager than the input with Logs_Intermediates taking up most the space. The script above could be modified to only transfer a subset of files back to shared storage.

Please send questions and comments to