kemal/SimurgArray
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details

Browse Source 
scripts/p8/prepare.py lays out the 360 GEO IDATs under their header barcode/position;
scripts/p8/validate_p8.py computes concordance, NRD, no-call rate, per-class and per-MAF
sensitivity/specificity/precision/F1 vs NYGC 30x and GIAB HG001, replicate concordance,
systematic/allele-swap site errors, per-chip batch table and duplicate detection.
Cloud userdata can skip the Omni2.5 archive (OMNI=0).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
This commit is contained in:
kemalandClaude Opus 5.5 committed 2026-09-28 17:43:31 +01:00
1 parent cd86681742
commit 70c36446a0
6 files changed
+1037 -6
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

scripts/cloud/userdata.sh
+8 -6
View File
@@ -47,12 +47,14 @@ mkdir -p refs && git clone -q --depth 1 https://github.com/Illumina/BeadArrayFil
SRC=s3://1000genomes/release/20130502/supporting/hd_genotype_chip/broad_intensities
D=/work/omni && mkdir -p $D/data
for f in HumanOmni2.5-4v1-Multi_B.bpm HumanOmni2.5-4v1-Multi_B.egt HumanOmni2.5-4v1_B.csv; do
$S3 cp --no-sign-request "$SRC/$f" $D/ --only-show-errors
done
echo "=== streaming 107 GB IDAT+GTC archive (no copy of the .tgz is kept) $(date -u +%T) ==="
$S3 cp --no-sign-request "$SRC/Omni25_idats_gtcs_2141_samples.tgz" - | pigz -dc | tar -x -C $D/data
echo "=== extracted $(du -sh $D/data | cut -f1) at $(date -u +%T) ==="
if [[ "__OMNI__" == "1" ]]; then
for f in HumanOmni2.5-4v1-Multi_B.bpm HumanOmni2.5-4v1-Multi_B.egt HumanOmni2.5-4v1_B.csv; do
$S3 cp --no-sign-request "$SRC/$f" $D/ --only-show-errors
done
echo "=== streaming 107 GB IDAT+GTC archive (no copy of the .tgz is kept) $(date -u +%T) ==="
$S3 cp --no-sign-request "$SRC/Omni25_idats_gtcs_2141_samples.tgz" - | pigz -dc | tar -x -C $D/data
echo "=== extracted $(du -sh $D/data | cut -f1) at $(date -u +%T) ==="
fi
echo "=== unit tests $(date -u +%T) ==="
.venv/bin/python -m pytest tests/unit -q -p no:cacheprovider || echo "unit tests reported failures (continuing)"