diff --git a/README.md b/README.md
index 1645a1b..2004bfd 100644
--- a/README.md
+++ b/README.md
@@ -25,19 +25,35 @@ From the raw article text, we generate the following features:
 
 ## Pipeline
 
-The pipeline contains two sets of python code:
+The pipeline contains four sets of python code:
 
-- `test_train.py`: this code takes a set of labeled cases with features and builds out test & train models. It can be used to run cross-validation on a selected model or to run the model loop.
-- `model_loop.py`: this code takes the output csvs from data_prep.py and runs them through various classification models. Results of those models performance on test sets is sent to an output csv for analysis. 
+- `model.py`: a class for models
+- `model_loop.py`: a class for running a loop of classifiers; takes test-train data splits and various run params
+- `run.py`: this code implements the model_loop class; it also implements our re-sampling of the data
+- `transform_features.py`: this file executes all feature generation
 
-We implement these two files differently via shell code depending on end goal. Each implementation will be named with its end goal in mind. 
+Running the code is done through `run.py` with the following options:
+
+1. `--models`: models to run
+2. `--iterations`: number of tuning parameter iterations to run per model
+3. `--output_dir`: a directory name to store the output; system will create the directory
+4. `--dedupe`: whether to look for and remove duplicate content
+5. `--features`: which feature set to run with, options include:  
+
+    - `both_only`: runs both PCFG and TFIDF
+    - `grammar_only`: runs only PCFG
+    - `tfidf_only`: runs only TFIDF
+    - `all`: runs all the above
 
 ## Example Pipeline Run
 
-To execute the pipeline with Logistic Regression and Naive Bayes, navigate to the pipeline directory, run:
+To execute the pipeline with Logistic Regression and Stochastic Gradient Descent, navigate to the pipeline directory, run:
+
 ```
-python run.py ../articles_deduped.csv --models LR NB
+source activate amlpp
+python run.py /path/to/data --models LR SGD --iterations 50 --output_dir run_name --dedupe --reduce 500 --features both_only
 ```
+This is encapsulated in the `run.sh` file. 
 
 The first argument is the path to the input datafile. The pipeline assumes that the text of each article is unique. If your texts are not unique, use the flag --dedupe to automatically remove duplicated articles during preprocessing. To see a description of all arguments, run: