Bit of restructuring

docs/configuration/reference_genomes.md

@@ -1,49 +0,0 @@
-# nf-core/atacseq: Reference Genomes Configuration
-
-The nf-core/atacseq pipeline needs a reference genome for alignment and annotation.
-
-These paths can be supplied on the command line at run time (see the [usage docs](../usage.md)),
-but for convenience it's often better to save these paths in a nextflow config file.
-See below for instructions on how to do this.
-Read [Adding your own system](adding_your_own.md) to find out how to set up custom config files.
-
-## Adding paths to a config file
-Specifying long paths every time you run the pipeline is a pain.
-To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline.
-
-Note that this genome key can also be specified in a config file if you always use the same genome.
-
-To use this system, add paths to your config file using the following template:
-
-```nextflow
-params {
-  genomes {
-    'YOUR-ID' {
-      fasta  = '<PATH TO FASTA FILE>/genome.fa'
-    }
-    'OTHER-GENOME' {
-      // [..]
-    }
-  }
-  // Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line
-  genome = 'YOUR-ID'
-}
-```
-
-You can add as many genomes as you like as long as they have unique IDs.
-
-## illumina iGenomes
-To make the use of reference genomes easier, illumina has developed a centralised resource called [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
-Multiple reference index types are held together with consistent structure for multiple genomes.
-
-We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default.
-The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon.
-The pipeline will automatically download the required reference files when you run the pipeline.
-For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/
-
-Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource.
-Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location.
-For example:
-```nextflow
-params.igenomes_base = '/path/to/data/igenomes/'
-```