Runs and reproducibility
Every oncology analysis step is a versioned pipeline run suitable for methods sections and audit trails.
Finding runs
| Location | What you see |
|---|---|
| Study overview — Run history | All pipeline runs for the study |
| Workflow pages | Latest completed run per pipeline type |
| Run detail | Full result summary and artifacts |
Run record
Each run stores:
- Pipeline type (cell communication, immune profile, mutation landscape, survival, interpret)
- Status, timestamps, and a run ID
- The parameters it was run with, and its pipeline version
- Result summary (TMB, interaction counts, KM groups, etc.)
- Downloadable artifacts
Provenance chains
Common chains:
interpret → mutation landscape / immune profile / cell communication / survival
survival → clinical endpoints + optional feature matrix from immune or mutation runs
mutation landscape → registered MAF dataset
cell communication → expression CSV + metadata CSV
immune profile → expression CSV (+ optional repertoire CSV)
Interpretation requires the source runs it cites to still exist and be complete.
Failed runs
Failed runs show an error message on the run detail page. Common causes:
- Missing required input file (mutation, clinical, or expression dataset)
- Expression/metadata CSV column mismatches for communication pipelines
- Empty or malformed MAF files
- A source run referenced by interpretation is missing or was deleted
Fix the underlying issue and re-run from the workflow page.
Versioning
Every run records a pipeline version. Include run IDs and versions in methods sections for reproducibility.
Re-running pipelines
Launch the same pipeline again with identical or updated parameters. A new run is created; the UI displays results from the latest completed run per pipeline type.