VirSieve¶

Description¶

Environmental Viral Detection pipeline. Contains VirSieveAlign, VirSieveGATK, VirSieveIVar, and VirSieveVEP applications

Environment Modules¶

Run module spider virsieve to find out what environment modules are available for this application.

Environment Variables¶

HPC_VIRSIEVE_DIR - installation directory
HPC_VIESIEVE_BIN - executable directory

Additional Usage Information¶

$ module load virseive/20210406 $ VirSieveIVar /blue/groupname/username/virsieve_test/

Each tool also has the ability to set non-default options via environment variables. Since we are running these tools w>```
$ module load virsieve/20210406
$ export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed
$ VirSieveIVar /blue/groupname/username/virsieve_test/

The expected working directory structure and lists of the available environment variables for each tool can be found on>https://www.github.com/Zymo-Research/VirSieveAlign https://www.github.com/Zymo-Research/VirSieveGATK https://www.github.com/Zymo-Research/VirSieveIVar https://www.github.com/Zymo-Research/VirSieveVEP https://www.github.com/Zymo-Research/VirSieveVEP

Job Script Examples¶

#!/bin/bash
#SBATCH --job-name=virsieve_test
#SBATCH --mail-type=NONE
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=4gb
#SBATCH --time=24:00:00
#SBATCH --output=virsieve_test.log

TEST_PWD=/data/apps/tests/virsieve
TEST_SAMPLEDIR=${TEST_PWD}/sample_data
TEST_WORKDIR=${TEST_PWD}/virsieve_test

cd ${TEST_PWD}
module load virsieve

# Remove any previous test results, create a working directory, and copy
# initial test reads into the expected position in working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir -p ${TEST_WORKDIR}/rawFASTQ
cp ${TEST_SAMPLEDIR}/*.gz ${TEST_WORKDIR}/rawFASTQ

echo "Starting test run at $(date) on $(hostname)..."

# Run VirSieveAlign (rawFASTQ/ --> processedFASTQ/, mergedBAM/, rawBAM/)
VirSieveAlign ${TEST_WORKDIR}

# Run VirSieveIVar (mergedBAM/ --> primerTrimBAM/)
# export SINGULARITYENV_PRIMERBED=/path/to/mycustom.bed
VirSieveIVar ${TEST_WORKDIR}

# Run VirSieveGATK (primerTrimBAM/ --> filteredVCF/, alignmentArtifactFilteredVCF/, etc.)
VirSieveGATK ${TEST_WORKDIR}

# Run VirSieveVEP (filteredVCF/, alignmentArtifactFilteredVCF/ --> vepOutputs/, results/)
VirSieveVEP ${TEST_WORKDIR}

# There should be some files in the results/ directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/results/ -type f ! -empty -ls

echo "Test complete at $(date)."

Categories¶

biology, pipeline