Test Nextflow Example Script

Test a Nextflow example script and verify it matches the documentation.

Working Directory

IMPORTANT: This skill works with directories in two phases:

1. Initial phase - Start from repository root

   • Repository root is the directory containing mkdocs.yml, docs/, and .github/
   • Verify you are in the correct directory (check for these files/folders)
   • Use this for finding scripts and reading documentation
   • All Grep and Glob operations use repository root paths

2. Execution phase - Change to the script's directory for running Nextflow

   • Use cd to the script's directory before running nextflow run
   • This ensures relative paths in the script work correctly