Documentation

**This repository was copied from https://github.com/bulatkhu/workflow-prototype on May 4th 2026

For comprehensive documentation, please see README.md

For a quick start guide, see QUICKSTART.md

Quick Reference

Basic Run

nextflow run main.nf -profile standard

Resume Interrupted Run

nextflow run main.nf -profile standard -resume

Prerequisites

Build Comet Search Docker Image (Optional)

If using mass spectrometry search functionality:

cd images
docker build -t comet:2025.03 .

Running in Background

To run the workflow in the background using screen:

1. Create a new screen: screen -S nf_run
2. Enter it: screen -r nf_run
3. Run your command: nextflow run main.nf -profile standard
4. To exit without killing the screen: Press Ctrl + A then d
5. To reattach later: screen -r nf_run