diff --git a/README.md b/README.md
index 64a092fbd9ad6482a7c3cac4b6b0570aa7743a20..6ea7f8f62733cd3984b836df404567f98a491236 100644
--- a/README.md
+++ b/README.md
@@ -7,4 +7,6 @@ This workflow takes as input:
  
  The output is a trancript sample gtf file and csv file containing transcript IDs and counts.
  
+ The workflow can be run via the command line as
  
+ python scripts/exe.py --annotation {gtf input file} --output_csv {output csv file} --transcript_number {number of transcripts} --output_gtf {output gtf file} --input_csv {input csv file}