run-pipeline

name	run-pipeline
description	Run the main.r pipeline and verify all outputs exist with non-zero size. Use to check that the full analysis reproduces correctly.
disable-model-invocation	true
argument-hint	[optional: specific script to run]

Run the R Analysis Pipeline

Run the project's R pipeline and verify outputs.

Steps

1. Identify what to run:

   • If $ARGUMENTS specifies a script: run that script only
   • Otherwise: run code/main.r (the full pipeline)

2. Execute the pipeline:

   Rscript code/main.r
   

   Or for a specific script:

   Rscript code/$ARGUMENTS
   

3. Verify outputs exist:

   • Check outputs/tables/ for expected table files (CSV, tex)
   • Check outputs/figures/ for expected figure files (PNG, PDF)
   • Check temp_data/ for intermediate datasets
   • Verify all output files have non-zero size

4. Report results:

   • Script exit code (0 = success)
   • List of output files created/updated with sizes
   • Any warnings or errors from R
   • Any missing expected outputs

5. If the pipeline fails:

   • Report the error message
   • Identify which script in the pipeline failed
   • Suggest likely causes