Add parabricks option

[genericdata]

https://docs.nvidia.com/clara/parabricks/latest/toolreference.html

Add a config option to use parabricks for supported processes such as gatk and bwa.

[genericdata]

It won't be a one to one process to process. For example, haplotypecaller for parabricks will run both gatk ApplyBSQR and gatk HaplotypeCaller which are separeted in two processed currently.

Parabricks Command

# This command assumes all the inputs are in INPUT_DIR and all the outputs go to OUTPUT_DIR.
docker run --rm --gpus all --volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
    pbrun haplotypecaller \
    --ref /workdir/${REFERENCE_FILE} \
    --in-bam /workdir/${INPUT_BAM} \
    --in-recal-file /workdir/${INPUT_RECAL_FILE} \
    --out-variants /outputdir/${OUTPUT_VCF}

Compatible GATK4 Command

# Run ApplyBQSR Step
$ gatk ApplyBQSR \
    --java-options -Xmx30g \
    -R Ref/Homo_sapiens_assembly38.fasta \
    -I mark_dups_cpu.bam \
    --bqsr-recal-file recal_file.txt \
    -O cpu_nodups_BQSR.bam

#Run Haplotype Caller
$ gatk HaplotypeCaller \
    --java-options -Xmx30g \
    --input cpu_nodups_BQSR.bam \
    --output result_cpu.vcf \
    --reference Ref/Homo_sapiens_assembly38.fasta \
    --native-pair-hmm-threads 16