8_run_dv.sl

#!/bin/bash -e

#SBATCH -A               xxxxxxxx
#SBATCH --cpus-per-task  16
#SBATCH --time           24:00:00
#SBATCH --mem            64G
#SBATCH --gpus-per-node  A100:1
#SBATCH --mail-user      p.tsai@auckland.ac.nz
#SBATCH -o               logs/%x.out
#SBATCH -e               logs/%x.err

module purge
module load Singularity
module load CUDA/11.4.1

export PYTHONNOUSERSITE=1
export SINGULARITY_BIND="/nesi/nobackup,/nesi/project"

REF=/refGenome/hg38/GRCh38_no_alt_plus_hs38d1_analysis_set/fasta/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna
OUTPUT_DIR=deepvariant_out

BAM=$1
SAMPLE=`basename ${BAM%.sorted.bam}`

# Create output folder for each sample separately
mkdir -p ${OUTPUT_DIR}/${SAMPLE}
CONTAINER=/opt/nesi/containers/DeepVariant/deepvariant-1.5.0-gpu.simg

singularity run --nv $CONTAINER \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS \
--ref=${REF} \
--reads=${BAM} \
--output_vcf=${OUTPUT_DIR}/${SAMPLE}/${SAMPLE}.vcf.gz \
--output_gvcf=${OUTPUT_DIR}/${SAMPLE}/${SAMPLE}.gvcf.gz \
--intermediate_results_dir=${OUTPUT_DIR}/${SAMPLE}/intermediate_results_dir \
--num_shards=${SLURM_CPUS_PER_TASK}