ogn-sdk (Python)
ogn-sdk is a tiny convenience layer around the ogn_run binary. Install it with:
python3 -m pip install ogn-sdk
Example usage:
from ogn_sdk import RunRequest, run_local
req = RunRequest(
fastq="/data/sample_R1.fastq.gz",
reference="/data/ref.fa",
output_vcf="out/sample.g.vcf.gz",
sample_id="hg002_chr20",
profile_dir="profile_hg002"
)
result = run_local(req)
print("exit status", result.returncode)
RunRequest maps directly to CLI flags, so you can pass fastq2, bundle, or
any additional CLI switches via extra_args. The helper simply shells out to
ogn_run (defaulting to the binary on PATH).
1 maintainer
Metadata
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Release files for ogn-sdk 0.9.1
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Total release size: 86.4 kB
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