IntOGen

:warning: Please note that IntOGen needs a lot of resources. We strongly suggest to run it in a cluster environment!

Install requirements

1. Install singularity (the pipeline has been tested with version 2.x)
2. Install nextflow (You can use conda install nextflow)
3. Clone this repository

Download and build prerequisites

The IntOGen pipeline requires a collection of datasets and Singularity containers in order to run.

:warning: The pipeline has been tested with hg38 and vep92 and vep101

See the README.rst file in the build folder for further details.

Then you can build all the datasets from the original sources. Note that this process can take a very long time and it might fail if the original sources had changed.

Run the pipeline

The IntOGen pipeline is built on top of nextflow. In order to execute the pipeline, you only need to execute:

nextflow run intogen.nf -resume -profile local --input test/ --output ./output

For further details, please check our documentation: http://intogen.rtfd.io/

To avoid stopping the pipeline execution for one or a few incorrect input, we have decided to ignore the errors of the steps by default. However, we advise to review each of them carefully to understand the underlying reasons.

Licensing

IntoGEn uses a variety of software tools and datasets that are released under a variety of licenses. In order to accommodate all of them, the pipeline itself is released under GNU General Public License version 3.

If you are using it for research/academic purposes it should be fine. For commercial usage, you need to revise the license of the different software pieces and datasets used, as some of them (e.g. CADD or CGC) are restricted for commercial usage.