P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task

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).

scripts/cloud/userdata.sh

@@ -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)"