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Recipe catalog — starting points

GENERATED from catalog.yaml by scripts/render_recipe_catalog.py — do not hand-edit.

The curated single source of truth is catalog.yaml. This list is deliberately small: it holds canonical starting points, not a record of every run (that is morphic-provenance). Provenance is the oracle for parameter values; a recipe's --profile/compose-up governs which output layers it emits. See AGENTS.md "Compose to the target".

id recipe modality engine minimal wrapper profiles compose-up provenance oracle composition examples status
multiome 10x Multiome (GEX + ATAC) — STAR GeneFull + Chromap ATAC + MACS peaks multiome scripts/run_star_multiome_lane_smoke.sh scripts/run_multiome_minimal.sh full, matrices-peaks ✓ runs/jax_multiome01 composition_morphic_jax_multiome01_20260517t183219z_star_multiome_prod_globus current
jax-multiome01-production MorPhiC jax_multiome01 production wrapper (pins the verified multiome config) multiome scripts/run_jax_multiome01_production.sh — — inherits runs/jax_multiome01 composition_morphic_jax_multiome01_20260517t183219z_star_multiome_prod_globus project-wrapper
scrnaseq-ocm 10x scRNA-seq (OCM) production batch — STARsolo GeneFull (+ Velocyto) scRNA-seq scripts/run_jax_scrnaseq02_ocm_production_batch.sh — — — runs/jax_scrnaseq02 composition_morphic_jax_scrnaseq02_20260522t135526z_ocm_prod_handoff current
scrna-downstream scRNA downstream — GeneFull+Velocyto h5ad + CellBender (remote, CUDA) scRNA-seq scripts/run_scrna_downstream_gene_full_velocyto.sh — — — runs/msk_30ko_revised — current
catatac-trimodal-e2e-smoke CAT-ATAC trimodal downsample E2E — RNA + ATAC + guide trimodal scripts/run_catatac_trimodal_downsample_smoke.sh — — ✓ multiomics-suite/docs/datasets/e2e_downsample_smoke_runs_20260617.md — current
dogma-hiv-four-arm-e2e-smoke DOGMA-HIV four-arm downsample E2E — RNA + ATAC + ADT + HIV state four-ome scripts/run_hiv_dogma_four_arm_downsample_smoke.sh — — ✓ multiomics-suite/docs/datasets/e2e_downsample_smoke_runs_20260617.md — current
trimodal-qc-report Trimodal MuData QC report — RNA + ATAC + guide multiomics-report scripts/generate_trimodal_qc.py — — ✓ multiomics-suite downstream MuData report recipes — current
four-factor-qc-report Four-factor MuData QC report — RNA + ATAC + protein + identity multiomics-report scripts/generate_four_factor_qc.py — — ✓ multiomics-suite downstream MuData report recipes — current
multiome-mudata-builder Multiome MuData builder — RNA + ATAC plus optional protein/guide/hash/state multiomics-builder scripts/build_multiome_mudata.py — — ✓ multiomics-suite/docs/runbooks/RUNBOOK_MULTIOME_MEX_MUDATA_20260516.md — current

Notes

  • multiome — Compose-up reference recipe. matrices-peaks = apples-to-apples with Cell Ranger ARC --no-bam + a Signac/MACS peak re-call; full = MorPhiC production superset (adds Velocyto + GEX BAM + Y/noY + remote downstream). Optional --chromap-macs3-frag-qvalue enables libchromap/MACS3 q-value peak selection without changing the default p-value mode.
  • jax-multiome01-production — Thin project wrapper of the multiome engine with the verified jax_multiome01 production parameters. Use the generic engine for new work.
  • scrnaseq-ocm — Compose-up RETROFIT candidate: Velocyto / BAM / remote downstream are optional layers that should become --profile/flags.
  • scrna-downstream — Compose-up RETROFIT candidate: CellBender / remote execution are optional layers. Needs CUDA for CellBender (see AGENTS.md CUDA policy).
  • catatac-trimodal-e2e-smoke — Paper-facing L1 reproducibility smoke. Runs the STAR-suite CAT-ATAC trimodal harness on a 100k downsample and then runs the standalone Signac/MACS BED-profile ATAC peak-MEX pass from the sidecar.
  • dogma-hiv-four-arm-e2e-smoke — Paper-facing L1 reproducibility smoke. Materializes matched physical first-N FASTQs for all FASTQ arms, runs the STAR-suite DOGMA table-backed four-arm harness, and then runs the standalone Signac/MACS BED-profile ATAC peak-MEX pass from the sidecar.
  • trimodal-qc-report — Downstream-from-MuData report recipe for the L4 agentic composability surface. It renders the unified trimodal QC from an assembled MuData object.
  • four-factor-qc-report — Downstream-from-MuData report recipe for the L4 agentic composability surface. It renders protein-aware four-factor QC from an assembled MuData object with optional guide/hash/state identity modalities.
  • multiome-mudata-builder — Public object-assembly recipe for Multiomics Suite outputs. Builds MuData from RNA and ATAC MEX inputs and can add protein/ADT, CRISPR guide, HTO/hash, and table-backed state modalities with feature-library provenance.

Not catalogued as starting points

Deliberately excluded to keep the list small (internal steps, smokes, remote executors, preflight, ops):

  • preflight: run_msk_30ko_fastq_preflight.sh, run_msk_40ko_fastq_preflight.sh
  • remote_executors: run_remote_cellbender_batch.sh, run_remote_cellbender_rsync.sh, run_remote_cellbender_scan.sh, run_remote_multiome_post_mex_rsync.sh, run_remote_scrna_downstream_rsync.sh
  • smokes: run_jax_scrnaseq02_ocm_composite_smoke.sh, run_jax_scrnaseq02_ocm_oracle_smoke.sh, run_multiome_mudata_smoke.sh
  • ops: backfill_jax_scrnaseq02_ocm_downstream.sh, upload_jax_multiome01_large_files_globus.sh

Elsewhere (suite-repo recipes / workflows)

Catalogued by each MCP server's list_workflows; cross-reference, do not duplicate:

  • STAR-suite/scripts/run_jax_scrnaseq01_flex_2024.sh (Flex; oracle runs/jax_scrnaseq01)
  • STAR-suite slam_seq_pe recipes (oracle runs/slam_seq_pe)
  • STAR-suite & Chromap-suite mcp_server/workflows/*.yaml (lower-level workflow schemas)