Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

umccrise: support presigned URL parsing #94

Merged
merged 8 commits into from
Sep 5, 2023
Merged

umccrise: support presigned URL parsing #94

merged 8 commits into from
Sep 5, 2023

Conversation

pdiakumis
Copy link
Member

Mainly adding functionality for parsing umccrise outputs (HRD/Sigs/QCsum) via presigned URLs.

  • read_tsvgz uses a gz connection prior to attempting to read the TSVs, in the same vein as described in Handle presigned URLs of gzipped JSONs #74.
  • glims_read is a convenience function for parsing the Google LIMS via {googlesheets}.
  • The umccrise metadata available from Athena (workflows table) is enough to grab LibraryID and SampleID for tumor and normal, except for those runs prior to 2023-04-07 (tumor SampleID is not available for those). We can instead use the LibraryID from the Google LIMS to map those and fill in the gaps.
  • Setting up an Rmd reporter for multiple umccrise results. Ingestion is actually pretty quick, a bit less than 1sec per file (449 successful umccrise runs x 5 files = 2,245 files from 2022-01-24 until 2023-09-03, excluding MultiQC results).

@pdiakumis
Copy link
Member Author

Merging, this looks good for now, added a funky HRD grouped plot.
Will try to grab older bcbio results too this week.

@pdiakumis pdiakumis merged commit 4436c11 into main Sep 5, 2023
1 check passed
@pdiakumis pdiakumis deleted the um_hrd_sig branch September 5, 2023 13:20
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant