updated readme

README.md

@@ -1,8 +1,21 @@
 # CTG_pipeline
 Data processing pipeline for PRISM CTG screens.
 
-To process raw data from a screen use `process_CTG.R`.
+To process raw data from a screen use `pipeline.sh` or `process_CTG.R`. Or using Docker run
+``` bash
+docker pull cmap/ctg:latest
+docker run -it
+  -v ~/ctg_data:/data
+  -v ~/ctg_results:/resuts \
+  cmap/ctg:latest \
+  -f data/mergedfile.csv \
+  -m data/mapping.csv \
+  -r data/raw_data.csv \
+  -o results \
+  -p <PROJECT>
+```
+replacing `<PROJECT>` with the name of the project and all other paths with the path to the appropriate data.
 
-To generate a report for a screen use `CTG_report.Rmd`.
+To generate a report for a screen use `CTG_report.Rmd` changing the data path parameter to point to processed CTG data.
 
-Docker image is on [Docker Hub](https://hub.docker.com/repository/docker/aboghoss/ctg)
+The Docker image is on [Docker Hub](https://hub.docker.com/repository/docker/cmap/ctg).