Hands-on experiment :mega:

NAIC Clara Parabricks

Installation: Clone NAIC Clara Parabricks GitHub ripository

# Clone NAIC Clara Parabricks GitHub ripository
git clone git@github.com:NAICNO/clara_parabricks.git

# NGS analysis workflows are available in `clara_parabricks/workflows`
cd clara_parabricks/workflows

Run command for GPU-only pipeline

bash nextflow-23.04.4-all \
    run \
    germline_pipeline.nf \
    -profile singularity \
    --fastq_folder <path to *fastq.gz files> \
    --genome_folder <path to GRCh38 reference files> \
    --genome_json reference_data.json \
    --processor GPU \
    -with-report \
    -with-trace \
    -resume

## Pipeline can use docker or singularity to run `parabricks` tools.
## Refere `README.md` for more details.

Reference datasets:

cat reference_data.json
{
    "known_sites_gold_standard": {
      "vcf": "Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
      "tbi": "Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"
    },
    "known_sites_high_confidence": {
      "vcf": "1000G_phase1.snps.high_confidence.hg38.vcf.gz",
      "tbi": "1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi"
    },
    "reference_fasta": {
      "fai": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai",
      "amb": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.amb",
      "pac": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.pac",
      "ann": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.ann",
      "bwt": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bwt",
      "sa": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.sa",
      "fna": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
      "dict": "GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.dict"
}

Implementation details - README.md

• https://github.com/NAICNO/clara_parabricks

Output

Results/GPU/
-- sample_name
    |-- alignments
    |   |-- sample_name_GPU_recal_gpu.txt -> <path to workfolder>/sample_name_GPU_recal_gpu.txt
    |   |-- sample_name_pbrun_fq2bam_GPU.bam -> <path to workfolder>/sample_name_pbrun_fq2bam_GPU.bam
    |-- variants
        |-- haplotypeCaller
            |-- sample_name_pbrun_fq2bam_GPU.bam.vcf -> <path to workfolder>/sample_name_pbrun_fq2bam_GPU.bam.vcf