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…ection output Collapse the 6 raw co_occurrence sections into a single multiqc_co_occurrence parent, each child keyed by its focal cell type (detected via interval-0 argmax) and downsampled to keep the prompt small. Tighten the analysis_instructions for co_occurrence, spatial_neighbors, and Moran's I to a fixed budget of top findings. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add a 'descriptor' param defaulting to the bundled descriptor_schema.json and stage it as a process input, so users can supply their own with --descriptor /path/to/theirs.json. Works on native and container profiles. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Pull request overview
This PR updates the llmize workflow to (1) collapse co-occurrence sections into a single focal-labeled section (mirroring spatial-neighbors), (2) cap/trim interpretation output via tighter descriptor instructions, and (3) shift primary usage to a Nextflow entrypoint with a configurable descriptor schema.
Changes:
- Add
--descriptorsupport end-to-end (Nextflow params + pipeline CLI) so users can provide custom descriptor schemas. - Collapse raw
co_occurrencesections into a singlemultiqc_co_occurrenceparent with per-focal children, and downsample co-occurrence curves to reduce prompt size. - Refresh README to focus on Nextflow usage and document parameters and file placement.
Reviewed changes
Copilot reviewed 6 out of 7 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| requirements.txt | Removes ToolUniverse-related optional deps; keeps core ollama client. |
| README.md | Switches primary run instructions to Nextflow; adds parameter table and file-placement guidance. |
| nextflow.config | Introduces params.descriptor defaulting to the bundled schema. |
| main.nf | Wires descriptor into the INTERPRET process and forwards --descriptor to pipeline.py. |
| json_reduction/reduction.py | Collapses co-occurrence sections into one focal-labeled section and downsamples curves. |
| json_reduction/descriptor_schema.json | Updates analysis instructions to constrain output for co-occurrence / Moran’s I / spatial neighbors. |
| interpret.py | Extends label collection to include multiqc_co_occurrence for glossary context. |
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| ch_input = channel.fromPath(params.input, checkIfExists: true) | ||
| ch_descriptor = channel.fromPath(params.descriptor, checkIfExists: true).first() | ||
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| INTERPRET(ch_input) | ||
| INTERPRET(ch_input, ch_descriptor) |
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Summary
Co-occurrence: collapse the 6 raw co_occurrence sections into one focal labeled section similar to how spatial neighbors was done. Trim co-occurrence / spatial-neighbors / Moran's I output to a fixed amount of top findings.
Nextflow: add a --descriptor param (defaults to our schema) so users can supply their own descriptors.
README: remove dead ToolUniverse and enrich content and the json_reduction tutorial; switch usage to Nextflow; add a parameter table and a "where to place your files" guide.