Change reference_genome outdir

IanKouzel · Feb 24, 2020 · 09a25f6 · 09a25f6
1 parent c4abdf8
commit 09a25f6
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/docs/output.md b/docs/output.md
@@ -291,7 +291,7 @@ You can skip this portion of the analysis by specifying the `--skip_merge_replic
     *Description*:  
     An IGV session file will be created at the end of the pipeline containing the normalised bigWig tracks, per-sample peaks, consensus peaks and differential sites. This avoids having to load all of the data individually into IGV for visualisation.
 
-    The genome fasta file required for the IGV session will be the same as the one that was provided to the pipeline. This will be copied into `reference_genome/` to overcome any loading issues. If you prefer to use another path or an in-built genome provided by IGV just change the `genome` entry in the second-line of the session file.
+    The genome fasta file required for the IGV session will be the same as the one that was provided to the pipeline. This will be copied into `genome/` to overcome any loading issues. If you prefer to use another path or an in-built genome provided by IGV just change the `genome` entry in the second-line of the session file.
 
     The file paths in the IGV session file will only work if the results are kept in the same place on your storage. If the results are moved or for example, if you prefer to load the data over the web then just replace the file paths with others that are more appropriate.
 
@@ -317,9 +317,9 @@ You can skip this portion of the analysis by specifying the `--skip_merge_replic
     Reference genome-specific files can be useful to keep for the downstream processing of the results.
 
     *Output directories*:
-    * `reference_genome/`  
+    * `genome/`  
       A number of genome-specific files are generated by the pipeline in order to aid in the filtering of the data, and because they are required by standard tools such as BEDTools. These can be found in this directory along with the genome fasta file which is required by IGV. If using a genome from AWS iGenomes and if it exists a `README.txt` file containing information about the annotation version will also be saved in this directory.  
-    * `reference_genome/BWAIndex/`  
+    * `genome/BWAIndex/`  
       If the `--save_reference` parameter is provided then the alignment indices generated by the pipeline will be saved in this directory. This can be quite a time-consuming process so it permits their reuse for future runs of the pipeline or for other purposes.  
 
 2. **Pipeline information**