update usage doc

docs/usage.md

@@ -25,30 +25,30 @@
 * [Hi-C specific options](#hi-c-specific-options)
     * [Reads mapping](#reads-mapping)
         * [`--bwt2_opts_end2end`](#--bwt2_opts_end2end)
-	* [`--bwt2_opts_trimmed`](#--bwt2_opts_trimmed)
-	* [`--min_mapq`](#--min_mapq)
+        * [`--bwt2_opts_trimmed`](#--bwt2_opts_trimmed)
+        * [`--min_mapq`](#--min_mapq)
     * [Digestion Hi-C](#digestion-hi-c)
         * [`--restriction_site`](#--restriction_site)
-	* [`--ligation_site`](#--ligation_site)
-	* [`--min_restriction_fragment_size`](#--min_restriction_fragment_size)
-	* [`--max_restriction_fragment_size`](#--max_restriction_fragment_size)
-	* [`--min_insert_size`](#--min_insert_size)
-	* [`--max_insert_size`](#--max_insert_size)
+        * [`--ligation_site`](#--ligation_site)
+        * [`--min_restriction_fragment_size`](#--min_restriction_fragment_size)
+        * [`--max_restriction_fragment_size`](#--max_restriction_fragment_size)
+        * [`--min_insert_size`](#--min_insert_size)
+        * [`--max_insert_size`](#--max_insert_size)
     * [Hi-C Processing](#hi-c-processing)
-	* [`--min_cis_dist`](#--min_cis_dist)
-	* [`--rm_singleton`](#--rm_singleton)
-	* [`--rm_dup`](#--rm_dup)
-	* [`--rm_multi`](#--rm_multi)
+        * [`--min_cis_dist`](#--min_cis_dist)
+        * [`--rm_singleton`](#--rm_singleton)
+        * [`--rm_dup`](#--rm_dup)
+        * [`--rm_multi`](#--rm_multi)
     * [Genome-wide contact maps](#genome-wide-contact-maps)
-	* [`--bins_size`](#--bins_size)
-	* [`--ice_max_iter`](#--ice_max_iter)
-	* [`--ice_filer_low_count_perc`](#--ice_filer_low_count_perc)
-	* [`--ice_filer_high_count_perc`](#--ice_filer_high_count_perc)
-	* [`--ice_eps`](#--ice_eps)
+        * [`--bins_size`](#--bins_size)
+        * [`--ice_max_iter`](#--ice_max_iter)
+        * [`--ice_filer_low_count_perc`](#--ice_filer_low_count_perc)
+        * [`--ice_filer_high_count_perc`](#--ice_filer_high_count_perc)
+        * [`--ice_eps`](#--ice_eps)
     * [Inputs/Outputs](#inputs-outputs)
         * [`--splitFastq`](#--splitFastq)
-	* [`--saveReference`](#--saveReference)
-	* [`--saveAlignedIntermediates`](#--saveAlignedIntermediates)
+        * [`--saveReference`](#--saveReference)
+        * [`--saveAlignedIntermediates`](#--saveAlignedIntermediates)
 * [Job resources](#job-resources)
 * [Automatic resubmission](#automatic-resubmission)
 * [Custom resource requests](#custom-resource-requests)