From e7e08935cf87bee33df51f887e66dc9fe33fb83d Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Wed, 17 Apr 2019 11:07:24 +0200
Subject: [PATCH] update usage doc
---
docs/usage.md | 36 ++++++++++++++++++------------------
1 file changed, 18 insertions(+), 18 deletions(-)
diff --git a/docs/usage.md b/docs/usage.md
index cda582e..15405ac 100644
--- a/docs/usage.md
+++ b/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)
--
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