Update README.md

README.md

-# GOSe-6mo-imputation
+# 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](https://zenodo.org/record/2641122) 
+(DOI: 10.5281/zenodo.2641122).
+
+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 startet, download the code and `cd` in the repository folder
+```bash
+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
+```bash
+./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 require
+that the Neurobot username and API token are available as environment variables
+```bash
+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
+```bash
+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
+```bash
+singularity exec container.sif snakemake impute
+```
+This produces a .html and a .csv file with imputed values in the subfolder 
+`output`.