testing git-internal links

README.md

@@ -48,10 +48,10 @@ Run a standard database search using the protein databases appended with candida
 A sample MaxQuant paramater file is provided in MaxQuant_templates. The output from this validation search is required to proceed with the next steps of the pipeline.
 
 ### Step 5. Quantify alterate decoding events
-The code for this step can be found in decode_pipeline/python_scripts. decode_pipeline/README.md contains detailed instructions for running this code.
+The code for this step can be found in decode_pipeline/python_scripts. [decode_pipeline/README.md](decode_pipeline/README.md) contains detailed instructions for running this code.
 
 ### Step 6. Downstream data analysis
-The data generated in the pipeline outlined above can be further analyzed in many ways. The code for the analysis described in [LINK TO PREPRINT] is compiled in ~/decode_analysis/ and [decode_figures](decode_figures).
+The data generated in the pipeline outlined above can be further analyzed in many ways. The code for the analysis described in [LINK TO PREPRINT] is compiled in [decode_analysis](decode_analysis) and [decode_figures](decode_figures).
 
 These directories contain different subsets of the analyses described in the paper along with the code to reproduce the figures. Each contain a README.md describing the analyses contained.