Comet (and Percolator) DDA Nextflow Documentation

This will run an automated Nextflow workflow that will run msconvert, Comet, Percolator, and (optionally) upload to Limelight for data analysis, sharing, and visualization. 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

• Comet (and Percolator) DDA Nextflow Documentation
• Workflow Overview
  • Workflow Components
  • How to Run
• How to Install the Workflow
  • If On Windows
  • Install Nextflow
  • Credentials
  • Optional: Set up AWS CLI on local system
  • Optional: Set up AWS credentials
  • Optional: Set up PanoramaWeb credentials
  • Optional: Set up Limelight 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 aws profile (AWS Batch)
  • The mail Section
• Output & Results
  • Command Line Output
  • Workflow Log
  • Workflow Results
  • Output Files
• How to Setup and Configure AWS Batch
  • Secrets on 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.