kemal
cbcb99f8d2
Found by the P10 fresh-VM run: `simurg inspect … | head` raised BrokenPipeError, reported as an internal error, and stopped examples/gsa_demo.sh (set -o pipefail). run_guarded now flushes stdout inside the guard and maps BrokenPipeError to ExitCode.SIGPIPE (141) without a message. p10.sh: SKIP_DOCKER/SKIP_CONDA, clearer digest report; p10t.sh runs build+pip+tutorial only.
Examples
| File | What it shows |
|---|---|
gsa_demo.sh |
End-to-end run on the public 36-sample GSA v4 PGx demo: genotype (GTC + QC) → qc report → gtc-to-vcf (per-sample VCF and cohort BCF) → export plink/bedgraph/finalreport → compare. Needs scripts/fetch_data.sh p0 and p6. bash examples/gsa_demo.sh results/gsa_demo 6 runs on the first 6 samples only. |
sample_sheet.csv |
Sample-sheet layout: key columns SentrixBarcode_A/SentrixPosition_A, reported sex, trio (Parent1/Parent2, used for Mendel errors), a replicate, and a free column (Batch) that is carried into the QC table. The sample identities in it are illustrative, not the real demo samples. |
The QC threshold profiles shipped with SimurgArray (src/simurg/qc/profiles/*.yaml) are the starting point for a
--qc-config file; simurg qc suggest-thresholds derives cohort-specific values. See docs/user_guide.md.