Skyline Import Targets Nextflow Documentation

This workflow will import spectra for pre-defined targets into a Skyline file and perform quantification of those targets. 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

• Skyline Import Targets Nextflow Documentation
• Workflow Overview
  • How to Run
  • Workflow Components
• How to Install the Workflow
  • If On Windows
  • Install Nextflow
  • Set up placeholder credentials
  • 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
  • Workflow Results
  • Output Files
• 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.