ritsushah/macrophage-trajectory-asbestos ? reverse-engineered prompt

Build me a reproducible single cell analysis project for the mouse lung dataset GSE127803, comparing asbestos exposed samples with the TiO2 control. I want the whole thing to run cleanly in Docker and through Nextflow, from downloading the data through quality control, integration, trajectory analysis, and final figures.

Please set it up so someone can open the repo, build the container, and run the workflow without guessing what to do next. Include a clear notebook for the final plots and summary tables, and make sure the pipeline saves processed data and publication ready outputs in the right folders. If you need to check current docs for any of the tools, feel free to look them up online.

The end result should help show the monocyte to macrophage fate split and highlight the profibrotic trajectory in a way that is easy to rerun and share.