Update docs

README.md

@@ -82,34 +82,38 @@ If you use a GENBANK or EMBL file the annotations will be used to annotate SNPs
 
 ### Generate the run folder
 
-This command will create a new folder with a Makefile in it:
+This command will create a new folder with a `Makefile` in it:
 
     nullarbor.pl --name PROJNAME --mlst saureus --ref US300.fna --input samples.tab --outdir OUTDIR
 
-### See some options
+This will check that everything is okay. One of the last lines it prints is the command you need to run
+to actually perform the analysis _e.g._
 
-Once set up, a Nullarbor folder can be used in a few different ways. 
-See what's available with this command:
+    Run the pipeline with: nice make -j 4 -C OUTDIR
 
-    make help
+So you can just cut and paste that:
 
-### Run
+    nice make -j 4 -C OUTDIR
 
-To actually run the analysis:
+The `-C` option just means to change into the `/home/maria/listeria/nullarbor` folder first, so you could 
+do this instead:
 
     cd OUTDIR
     make 
 
-Or if you want to run parallel jobs:
-
-    make -C OUTDIR -j 8
-
 ### View the report
 
     firefox OUTDIR/report/index.html
 
 An example report will be made available soon.
 
+### See some options
+
+Once set up, a Nullarbor folder can be used in a few different ways. 
+See what's available with this command:
+
+    make help
+
 ## Etymology
 
 The [Nullarbor](http://en.wikipedia.org/wiki/Nullarbor_Plain)