Carafe Nextflow Documentation

This workflow is designed to go from RAW files to an AI-enhanced spectral library using the Carafe tool for experiment-specific in silico spectral library generation for DIA data analysis. See https://github.com/Noble-Lab/Carafe for more information.

This workflow supports starting with Thermo RAW (.raw), Bruker raw (.d or .d.zip), or mzML files and a FASTA file. It will run msconvert (for Thermo RAW) or unzip (for Bruker .d.zip) as needed, and DIA-NN to generate a peptide report for input to Carafe; or you may start with a peptide report previously generated with DIA-NN to skip running DIA-NN. See Workflow Parameters for more information.

Please use the links below to navigate to pages describing how to install and run the workflow, how to retrieve results, and how to set up AWS Batch to run the workflow in the cloud.

Getting Help, Providing Feedback, or Reporting Problems

If you need help, have ideas for new features, encounter a problem, or have any questions or comments, please contact Michael Riffle at mriffle@uw.edu.

Documentation Sections

• Carafe Nextflow Documentation
• Workflow Overview
  • How to Run
  • Workflow Components
• How to Install the Workflow
  • If On Windows
  • Install Nextflow
  • Optional: Set up AWS CLI on local system
  • Optional: Set up AWS credentials
  • Optional: Set up PanoramaWeb credentials
  • Optional: Install Docker on local system
  • Optional: Set up Docker credentials
• How to Run the Workflow
• Workflow Parameters
  • The params Section
  • The profiles Section
  • The mail Section
• Output & Results
  • Command Line Output
  • Workflow Log
  • Output Files
• Using a Custom DIA-NN Version
  • Prerequisites
  • Step 1: Download the Build Script
  • Step 2: Run the Build Script
  • Step 3: Configure the Workflow
  • Verifying the Version
• How to Setup and Configure AWS Batch

Funding & Attribution

This work was made possible with funding from IARPA via the TEI-REX program (Contract #: W911NF2220059). The contents of these documents are purely technical in nature, with no opinions or perspectives of the US Goverment’s interests in TEI-REX.