Add reference snippet. Close #85.

CHANGELOG.md

-# v0.1.0 (in development)
+# v1.0.0 (in development)
 **User Facing**
 * Add option to pull references from datahub
 * Add option to send email on workflow error, with pipeline error message
@@ -17,6 +17,7 @@
 * Error if pe and line count of R1 != R2
 * Error if ambiguous species inference
 * Remove non fastq from inputBag from the export bag config level
+* Add link to reference builder script
 
 **Background**
 * Remove (comment out) option to pull references from S3

README.md

@@ -75,6 +75,11 @@ FULL EXAMPLE:
 nextflow run workflow/rna-seq.nf --repRID Q-Y5JA --source production --deriva ./data/credential.json --bdbag ./data/cookies.txt --dev false --upload true -profile biohpc
 ```
 
+To generate you own references or new references:
+------------------------------------------
+Download the [reference creation script](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/snippets/31).
+This script will auto create human and mouse references from GENCODE. It can also create ERCC92 spike-in references as well as concatenate them to GENCODE references automatically. In addition, it can create references from manually downloaded FASTA and GTF files.
+
 To run a set of replicates from study RID:
 ------------------------------------------
 Run in repo root dir: