Output Layout

Every run writes into a standardized output root.

Top-level layout

  • qc/

  • work/normalized/

  • work/magma/

  • work/features/

  • work/pops/

  • tables/

  • reports/

  • metadata/

What each section contains

qc/

  • input validation summaries

  • resource resolution QC summaries

work/magma/

  • MAGMA annotation products

  • <trait>.genes.out

  • <trait>.genes.raw

work/features/

  • munged PoPS feature matrices

  • .rows.txt

  • .cols.*.txt

  • .mat.*.npy

work/pops/

  • <trait>.preds

  • <trait>.coefs

  • <trait>.marginals

tables/

  • prioritized_genes.tsv

  • all_genes_ranked.tsv

  • top_features.tsv

reports/

  • report.html

  • summary.json

metadata/

  • resolved_manifest.yaml

  • run_metadata.json

  • software_versions.json

Why this layout matters

The standardized layout keeps intermediate products inspectable while still supporting a simple end-to-end CLI. It also makes stage reruns predictable:

  • reporting can rerun from existing PoPS outputs

  • prioritization can rerun with different locus definitions

  • manifests and metadata preserve provenance for debugging and reproducibility