updated README

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}