synthesize-paper-rough

Metadata

Description

READ FIRST: paper_prep/synthesis/ARCHITECT_TASK_BRIEF.md (full task brief).
SHORT VERSION: Read ALL paper_prep/surveys/SURVEY_*.md files. Produce four deliverables:
  A. paper_prep/synthesis/MANUSCRIPT_SKELETON.md — Nature-format skeleton with exactly 4 main figures and 6-10 Extended Data figures, full panel descriptions, status (READY/GENERATE) per figure.
  B. paper_prep/synthesis/TALK_OUTLINE_15MIN.md — 12-14 slides keyed to main figures.
  C. paper_prep/synthesis/WORK_DECOMPOSITION.md — Phase-3 (figures) and Phase-4 (validation) task list.
  D. Dispatch all Phase-3 and Phase-4 tasks via 'wg add' (tag paper-prep,figure or paper-prep,validation; each task description must include the relevant excerpt of MANUSCRIPT_SKELETON.md so agents see their slot). Add a final 'compile-manuscript-draft' integrator task with --after over all phase-3/4 tasks.
GUARDRAILS: keep total Phase-3/4 task count under 15 (group panels into single tasks if needed). Do NOT propose new wet-lab or large new computational analyses; flag gaps in WORK_DECOMPOSITION.md if any.
ACCEPTANCE: 4 files exist as specified, all dispatched tasks visible in 'wg list'. See ARCHITECT_TASK_BRIEF.md for full details.

Depends on

• done survey-mouse-cross
• done survey-figure-inventory
• done survey-rpe-1-self
• done survey-pedigree-recombination
• done survey-integrated-interpretation
• done survey-cytogenetic-fish
• done survey-pipeline-section
• done survey-annotation-section
• done survey-gene-enrichment
• done survey-heterogeneity-section
• done survey-hi-c
• done survey-dip-c
• done survey-data-table
• done survey-limitations-summary
• done .assign-synthesize-paper-rough

Required by

• done .flip-synthesize-paper-rough
• done figure-1-landscape-communities
• done figure-2-heterogeneity-population
• done figure-3-3d-convergence
• done figure-4-pedigree-mouse
• done figure-ed1-ed2-pipeline-seqlevel
• done figure-ed3-ed4-annotation-genes
• done figure-ed5-hic-robustness
• done figure-ed6-ed7-singlecell-mouse
• done figure-ed8-discussion-models
• done validate-acceptance-checklist
• done validate-captions-references
• done validate-reproducibility-paths
• done validate-statistics-fdr-cis

Log

• 2026-05-05T04:26:04.897895346+00:00 Task paused
• 2026-05-05T04:37:00.002121685+00:00 Task published
• 2026-05-05T04:37:18.784932918+00:00 Lightweight assignment: agent=random-agent-327a66f9 (327a66f9), exec_mode=full, context_scope=graph, reason=Task explicitly requires architectural thinking for paper skeleton design, figure layout, and work decomposition; Architect role matches perfectly, and graph scope handles 15+ survey dependencies with task dispatch coordination
• 2026-05-05T04:40:18.081536930+00:00 Spawned by coordinator --executor claude --model opus
• 2026-05-05T04:40:36.829298212+00:00 Starting: ARCHITECT_TASK_BRIEF.md absent — proceeding from SHORT VERSION in task description. 13 surveys present in paper_prep/surveys/.
• 2026-05-05T05:19:19.038587687+00:00 Validated all 4 deliverables: A. MANUSCRIPT_SKELETON.md (Nature article skeleton, 4 main figs + 8 ED figs, panel-level status READY/GENERATE per skeleton); B. TALK_OUTLINE_15MIN.md (14 slides keyed to main figs); C. WORK_DECOMPOSITION.md (9 figure tasks + 4 validation + 1 integrator = 14 dispatched, under 15 cap); D. Dispatched all 13 worker tasks + 1 integrator with --after over all 13. Integrator deps verified via wg show.
• 2026-05-05T05:21:46.703745777+00:00 Committed: 0f16e4b — pushed to origin/wg/agent-682/synthesize-paper-rough. 14 tasks dispatched and verified in wg list. Final acceptance: 4 deliverable files exist; integrator compile-manuscript-draft has --after over all 13 workers.
• 2026-05-05T05:21:51.528588393+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
• 2026-05-05T05:25:30.827105795+00:00 PendingEval → Done (evaluator passed; downstream unblocks)