From 7ba128bea7d130a98cf64d4d36d74514338ca4a9 Mon Sep 17 00:00:00 2001 From: Rotholandus Date: Fri, 10 Aug 2018 11:40:08 +0200 Subject: [PATCH] Missing likns fixed in usage.md --- docs/usage.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index ab84e6f9..9da833cd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,7 +6,7 @@ * [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) @@ -14,13 +14,12 @@ * [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