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).
This commit is contained in:
1 parent
b699d2c188
commit
8cc1e52f69
6 files changed
+1037
-6
No files matched your search
@@ -64,7 +64,9 @@ launch)
|
||||
git archive --format=tar.gz -o /tmp/simurg-repo.tar.gz HEAD
|
||||
$AWS s3 cp /tmp/simurg-repo.tar.gz "s3://$BUCKET/$RUN/repo.tar.gz" --only-show-errors
|
||||
[[ -f scripts/cloud/tasks/$TASK.sh ]] || { echo "unknown TASK $TASK"; exit 2; }
|
||||
OMNI=${OMNI:-1} # 0: the task does not need the 107 GB Omni2.5 archive
|
||||
sed -e "s/__BUCKET__/$BUCKET/" -e "s/__RUN__/$RUN/" -e "s/__MAX_MINUTES__/$MAX_MINUTES/" -e "s/__TASK__/$TASK/g" \
|
||||
-e "s/__OMNI__/$OMNI/" \
|
||||
scripts/cloud/userdata.sh > /tmp/simurg-userdata.sh
|
||||
AMI=$($AWS ssm get-parameter --name /aws/service/canonical/ubuntu/server/24.04/stable/current/arm64/hvm/ebs-gp3/ami-id \
|
||||
--query Parameter.Value --output text)
|
||||
|
||||
Reference in new issue
Block a user