GOSe 6mo imputation for CENTER-TBI

This repository contains the code for imputing the 6 months GOSe using a multi-state model in CENTER-TBI. The workflow is completely automated using snakemake and a singularity container with the required dependencies is awailable at zenodo.org (DOI: 10.5281/zenodo.2641161).

Singularity >= 2.6.0 is required to run the code in a container, alternatively the dependencies can be installed manually (check the container-recipe file).

To get started, download the code and cd in the repository folder

git clone https://git.center-tbi.eu/kunzmann/gose-6mo-imputation-production.git
cd gose-6mo-imputation-production

Next, download the pre-build container image from zenodo.org via the provided script

./scripts/download-container

This will download the container.sif file (~1Gb) in the current working directory. An automated download script via the Neurobot-API is provided but requires that the Neurobot username and API token are available as environment variables

export NEUROBOT_USR=[your-neurobot-username]
export NEUROBOT_API=[your-neurobot-api-token]

The required data set (for version 1.2 on the Neurobot staging server) can then automatically be downloaded via

singularity exec container.sif snakemake download

Alternatively, a .csv file with the correct column names / ordering can directly be places in the data subfolder (see scripts/check-inputs for detailed specification). The imputation can then be started by invoking

singularity exec container.sif snakemake impute

This produces a .html and a .csv file with imputed values in the subfolder output.