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Casanovo Nextflow Workflow Documentation
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This Nextflow workflow automates the running of Casanovo and, optionally, the upload of the results to Limelight for visualization and sharing. There is no need for you to install Casanovo, Python, msconvert,
Java, Limelight, or any other software required by the workflow components. These documents describe how to install and run the workflow and how to retrieve results. The source code for the workflow can be found at: 
https://github.com/mriffle/nf-ms-dda-casanovo. 

**Casanovo** (https://github.com/Noble-Lab/casanovo) is an AI/deep learning tool for performing *de novo* identification of peptides present in bottom up mass spectrometry proteomics data—so-called DDA mass spectrometry data.

**Limelight** (https://limelight-ms.org/) is a general web application for searching, visualizing, sharing, and analyzing proteomics search results from any software pipeline. You may view Peptides, PSMs, and proteins; annotated
MS2 and MS1 scans; QC and statistics visualizations; share data with collaborators or for publication; compare searches; and more. To ensure data provenance, all configuration and Casanovo log
files are also uploaded to Limelight.

Please use the links below to navigate to pages describing how to install and run the workflow and how to retrieve results. If you would like to run in the cloud, we have included documentation for how to set up AWS Batch.

Getting Help, Providing Feedback, or Reporting Problems
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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
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.. toctree::
   :maxdepth: 2

   self
   overview
   how_to_install
   how_to_run
   workflow_parameters
   results
   set_up_aws