Examples

Example pipelines

Use these starting points to wire OGN into your workflows.

Nextflow WGS

nextflow run ogn-wgs/main.nf   --reads 's3://datasets/hg002/R{1,2}.fastq.gz'   --ref s3://refs/grch38_noalt.fa   --export vcf,metrics.json   --verify veribiota:giab-hg002

Wraps OGN submit under the hood; produces VCF, metrics, and VeriBiota report.

Snakemake drop-in

rule ogn_wgs:
  input:
    R1="s3://datasets/hg002/R1.fastq.gz",
    R2="s3://datasets/hg002/R2.fastq.gz",
    ref="s3://refs/grch38_noalt.fa"
  output:
    "results/hg002.vcf",
    "results/metrics.json"
  shell:
    "ogn submit --reads {input.R1} --reads {input.R2} --ref {input.ref} --pipeline wgs30 --export vcf,metrics.json --verify veribiota:giab-hg002"