Move index discussion earlier

Author: pinin4fjords

docs/usage.md

@@ -155,6 +155,15 @@ Notes:
 - If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
 - When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568)).
 
+#### Indices
+
+By default, indices are generated dynamically by the workflow for tools such as STAR and Salmon. Since indexing is an expensive process in time and resources you should ensure that it is only done once, by retaining the indices generated from each batch of reference files:
+
+- the `--save_reference` parameter will save your indices in your results directory
+- the `--skip_alignment --skip_pseudo_alignment` will disable other processes if you'd like to do an 'indexing only' workflow run. 
+
+Once you have the indices from a workflow run you should save them somewhere central and reuse them in subsequent runs using custom config files or command line parameters such as `--star_index '/path/to/STAR/index/'`.
+
 #### Gencode
 
 If you are using [GENCODE](https://www.gencodegenes.org/) reference genome files please specify the `--gencode` parameter because the format of these files is slightly different to ENSEMBL genome files:
@@ -173,15 +182,6 @@ This pipeline uses featureCounts to generate QC metrics based on [biotype](http:
 
 Please get in touch with us on the #rnaseq channel in the [nf-core Slack workspace](https://nf-co.re/join) if you are having problems or need any advice.
 
-#### Indices
-
-By default, indices are generated dynamically by the workflow for tools such as STAR and Salmon. Since indexing is an expensive process in time and resources you should ensure that it is only done once, by retaining the indices generated from each batch of reference files:
-
-- the `--save_reference` parameter will save your indices in your results directory
-- the `--skip_alignment --skip_pseudo_alignment` will disable other processes if you'd like to do an 'indexing only' workflow run. 
-
-Once you have the indices from a workflow run you should save them somewhere central and reuse them in subsequent runs using custom config files or command line parameters such as `--star_index '/path/to/STAR/index/'`.
-
 ### iGenomes (not recommended)
 
 If the `--genome` parameter is provided (e.g. `--genome GRCh37`) then the FASTA and GTF files (and existing indices) will be automatically obtained from AWS-iGenomes unless these have already been downloaded locally in the path specified by `--igenomes_base`.