Sniffles2 Job Scripts

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Job Script used for testing application installation

#!/bin/bash
#SBATCH --job-name=sniffles2_2.0.6_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=24:00:00
#SBATCH --output=sniffles2_2.0.6_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/sniffles2/2.0.6
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load sniffles2/2.0.6

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}

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

###################################
sniffles \
    --input ${TEST_DATADIR}/mapt.NA12156.altex.bam \
    --vcf ${TEST_WORKDIR}/test1.vcf.gz \
    --snf ${TEST_WORKDIR}/test1.snf \
    --threads ${SLURM_CPUS_ON_NODE:-4}
###################################

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

echo "Test complete at $(date)."