solve #36

pipeline/README.md

@@ -42,6 +42,7 @@ profiles {
 }
 
 ```
+Input files generally are placed in the two folders `data_dir_bulk` (for bulk mixtures) and `data_dir_sc` (for scRNA-seq references). The bulk datasets and scRNA-seq annotations we used during the omnideconv benchmarking efforts can be found at https://figshare.com/projects/deconvData/197794. The count matrices of the references should be accessed individually from the original data sources and can be preprocessed like we describe in our omnideconv benchmarking manuscript.
 Running the pipeline with the above configuration will expect the following folder structure: