Merge pull request #42 from Rotholandus/master

Missing likns fixed in usage.md

Author: ewels

docs/usage.md

@@ -6,21 +6,20 @@
 * [Input Data](#input-data)
 * [Reference Genomes](#reference-genomes)
     * [`--genome`](#--genome)
-    * [Supplying reference indices](#supplying-reference-indices)
+    * [Supplying reference indices](#--bwa_index)
     * [`--saveReference`](#--savereference)
 * [Adapter Trimming](#adapter-trimming)
 * [`--notrim`](#--notrim)
 * [Job Resources](#job-resources)
     * [Automatic resubmission](#automatic-resubmission)
     * [Maximum resource requests](#maximum-resource-requests)
 * [Other command line parameters](#other-command-line-parameters)
-    * [`-name`](#-name-single-dash)
-    * [`-resume`](#-resume-single-dash)
+    * [`-name`](#-name)
+    * [`-resume`](#-resume)
     * [`--email`](#--email)
     * [`--plaintext_email`](#--plaintext_email)
-    * [`-c`](#-c-single-dash)
+    * [`-c`](#-c)
     * [`--multiqc_config`](#--multiqc_config)
-    * [`--project`](#--project)
     * [`--clusterOptions`](#--clusteroptions)
 
 ## Running the pipeline