Demonstration

A LENS demonstration provides an end-to-end example of the LENS workflow being run on a melanoma patient (Pt01) from the dataset associated with Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma (Hugo et al., 2006).

This demonstration provides users an opportunity to see a comprehensive example of how LENS processes data through its workflows using real patient data. Furthermore, it provides example outputs so users can determine is running LENS is appropriate for their analysis.

To run LENS in demonstration mode, users should install and setup RAFT (see Installing RAFT), cd to their raft/ directory, and run:

raft.py run-demo \
  --workflow lens \
  --version 1.5-dev

This will:

  • Create a project named demo-lens in ./raft/projects

  • Download the required RAFT modules

  • Download the demo references, sample-level FASTQS, and sample manifest

  • Run the project’s workflow

During execution, users will see progress messages such as:

Initializing project demo-lens...
Pulling off-the-shelf workflow...
This may take some time due to module fetching.
Loading manifest...
Loading references...
...
All human references downloaded successfully!
Loading fastqs...
Building workflow...
Connecting subworkflows...
Populating default parameters...
Running workflow...

The resulting project will be stored in /path/to/raft/projects/demo-lens-v1.4/.

The outputs from LENS will be available in /path/to/raft/projects/demo-lens-v1.4/outputs

The LENS report can be found in /path/to/raft/projects/demo-lens-v1.4/outputs/lens/.

Information regarding LENS outputs can be found at :doc:outputs.

Detailed descriptions of the LENS reports and its components are available at LENS Report.