Create README.md

README.md

+# CENTER-TBI six-months GOSe-Outcome Imputation
+
+# Prerequisites
+
+We assume a Unix command line workflow. The following software is required to take advantage of the pre-defined workflow:
+  * [python](https://www.python.org/download/releases/3.5.1/) 3.5.1 (higher versions might work as well) 
+  * [snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) version 5.2.1 (higher versions will work as well)
+  * [singularity](https://www.sylabs.io/guides/2.6/user-guide/index.html) 2.6.0 (higher versions might work as well)
+
+The entire analysis is containerized using a [docker container](https://cloud.docker.com/u/kkmann/repository/docker/kkmann/gose-6mo-imputation). 
+The container can either be used to execute scripts individually inside the container, or it can be used to run the entire 
+pre-defined snakemake workflow using the container via singularity (recommended).
+A [script](https://github.com/kkmann/center-6mo-gose-imputation/blob/master/snakemake_slurm) for running the entire analysis 
+on a slurm cluster is provided. 
+Make sure to adjust the parameters in the [cluster configuration file](https://github.com/kkmann/center-6mo-gose-imputation/blob/master/cluster.json) 
+accordingly.
+
+A [script](https://github.com/kkmann/center-6mo-gose-imputation/blob/master/snakemake) for execution on a single desktop 
+machine is provided as well. Depending on the number of cores and available RAM, the cross-validated model comparison may take several 
+days (3+) to complete.
+The script can be invoked via
+```
+./snakemake_slurm [target]
+```
+where `[target]` is the build target (e.g. 'data_report_v1_1').
+
+
+# Executing the workflow
+
+The available rules can be listed by invoking
+```
+snakemake -lt
+```
+
+
+To reproduce the data extraction an population description on version v1.1 of the neurobot CENTER-TBI data, invoke 
+```
+./snakemake_slurm data_report_v1_1
+```
+
+To reproduce the cross-validated model comparison on version v1.1 of the neurobot CENTER-TBI data, invoke 
+```
+./snakemake_slurm cv_model_comparison_report_v1_1
+```
+
+
+To reproduce the MSM model-based imputation for v1.1 of the neurobot CENTER-TBI data, invoke 
+```
+./snakemake_slurm cv_model_comparison_report_v1_1
+```