Fix usage

nf-core · Dec 9, 2019 · 0946c41 · 0946c41
1 parent dd024d2
commit 0946c41
Showing 1 changed file with 34 additions and 34 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -9,50 +9,50 @@
     * [Updating the pipeline](#updating-the-pipeline)
     * [Reproducibility](#reproducibility)
   * [Main arguments](#main-arguments)
-    * [`-profile`](#profile)
-    * [`--reads`](#reads)
-    * [`--aligner` (Required)](#aligner-required)
+    * [-profile](#-profile)
+    * [--reads](#--reads)
+    * [--aligner (Required)](#--aligner-required)
       * [Alevin](#alevin)
-        * [`--salmon_index`](#salmonindex)
-        * [`--txp2gene_alevin`](#txp2genealevin)
+        * [--salmon_index](#--salmon_index)
+        * [--txp2gene_alevin](#--txp2gene_alevin)
       * [STARSolo](#starsolo)
-        * [`--star_index`](#starindex)
+        * [--star_index](#--star_index)
       * [Kallisto | BUStools](#kallisto--bustools)
-        * [`--bustools_correct`](#bustoolscorrect)
-        * [`--skip_bustools`](#skipbustools)
-        * [`--kallisto_gene_map`](#kallistogenemap)
-        * [`--kallisto_index`](#kallistoindex)
+        * [--bustools_correct](#--bustools_correct)
+        * [--skip_bustools](#--skip_bustools)
+        * [--kallisto_gene_map](#--kallisto_gene_map)
+        * [--kallisto_index](#--kallisto_index)
     * [Cellular barcodes](#cellular-barcodes)
-      * [`--type` to specify droplet type (Required)](#type-to-specify-droplet-type-required)
-      * [`--chemistry` (using cellranger barcodes) (Required)](#chemistry-using-cellranger-barcodes-required)
-      * [`--barcode_whitelist` for custom barcode whitelist](#barcodewhitelist-for-custom-barcode-whitelist)
+      * [--type to specify droplet type (Required)](#--type-to-specify-droplet-type-required)
+      * [--chemistry (using cellranger barcodes) (Required)](#--chemistry-using-cellranger-barcodes-required)
+      * [--barcode_whitelist for custom barcode whitelist](#--barcode_whitelist-for-custom-barcode-whitelist)
   * [Reference genomes](#reference-genomes)
-    * [`--genome` (using iGenomes)](#genome-using-igenomes)
-    * [`--fasta`](#fasta)
-    * [`--gtf`](#gtf)
-    * [`--transcriptome_fasta`](#transcriptomefasta)
-    * [`--save_reference`](#savereference)
-    * [`--igenomes_ignore`](#igenomesignore)
+    * [--genome (using iGenomes)](#--genome-using-igenomes)
+    * [--fasta](#--fasta)
+    * [--gtf](#--gtf)
+    * [--transcriptome_fasta](#--transcriptome_fasta)
+    * [--save_reference](#--save_reference)
+    * [--igenomes_ignore](#--igenomes_ignore)
   * [Job resources](#job-resources)
     * [Automatic resubmission](#automatic-resubmission)
     * [Custom resource requests](#custom-resource-requests)
   * [AWS Batch specific parameters](#aws-batch-specific-parameters)
-    * [`--awsqueue`](#awsqueue)
-    * [`--awsregion`](#awsregion)
+    * [--awsqueue](#--awsqueue)
+    * [--awsregion](#--awsregion)
   * [Other command line parameters](#other-command-line-parameters)
-    * [`--outdir`](#outdir)
-    * [`--email`](#email)
-    * [`-name`](#name)
-    * [`-resume`](#resume)
-    * [`-c`](#c)
-    * [`--custom_config_version`](#customconfigversion)
-    * [`--custom_config_base`](#customconfigbase)
-    * [`--max_memory`](#maxmemory)
-    * [`--max_time`](#maxtime)
-    * [`--max_cpus`](#maxcpus)
-    * [`--plaintext_email`](#plaintextemail)
-    * [`--monochrome_logs`](#monochromelogs)
-    * [`--multiqc_config`](#multiqcconfig)
+    * [--outdir](#--outdir)
+    * [--email](#--email)
+    * [-name](#-name)
+    * [-resume](#-resume)
+    * [-c](#-c)
+    * [--custom_config_version](#--custom_config_version)
+    * [--custom_config_base](#--custom_config_base)
+    * [--max_memory](#--max_memory)
+    * [--max_time](#--max_time)
+    * [--max_cpus](#--max_cpus)
+    * [--plaintext_email](#--plaintext_email)
+    * [--monochrome_logs](#--monochrome_logs)
+    * [--multiqc_config](#--multiqc_config)
 
 ## Introduction