Getting Started

The analysis software provided in this repository is implemented in the open-source workflow management software tool Nextflow. Please follow the instructions provided by that community to install Nextflow appropriately for your computational resources (laptop, HPC, cloud, etc.). With that installation in place, Geneshot can be run with the base command nextflow run Golob-Minot/geneshot <ARGS>, filling in the arguments as described in the remainder of this documentation.

Here are some links which should help you getting started with Nextflow:

• Nextflow Home Page
• Nextflow Documentation
• Using Nextflow at Fred Hutch

When you are setting up Nextflow to use geneshot, you will need to answer the following questions:

• What computational resources ("executor") am I going to use to process the data?
• Where is my input data located?
• Where do I want to store the results?
• Where can I keep temporary data generated during the course of the workflow? (note: the -work-dir used during execution can be safely deleted once the workflow has completely finished).

Once you have everything installed, perform a quick test by running:

nextflow run Golob-Minot/geneshot --help

You should see a helpful message describing all of the options needed for Running Geneshot