Add note about differing STAR indices versions

CHANGELOG.md

@@ -13,7 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * Updated pipeline template to nf-core/tools `1.12.1`
-* [[#499][https://github.com/nf-core/rnaseq/issues/499]] - Use of salmon counts for DESeq2
+* [[#498](https://github.com/nf-core/rnaseq/issues/498)] - Significantly different versions of STAR in star_rsem (2.7.6a) and star (2.6.1d)
+* [[#499](https://github.com/nf-core/rnaseq/issues/499)] - Use of salmon counts for DESeq2
 * [[#500](https://github.com/nf-core/rnaseq/issues/500), [#509](https://github.com/nf-core/rnaseq/issues/509)] - Error with AWS batch params
 * [[#511](https://github.com/nf-core/rnaseq/issues/511)] - rsem/star index fails with large genome
 * [[#515](https://github.com/nf-core/rnaseq/issues/515)] - Add decoy-aware indexing for salmon

README.md

@@ -49,6 +49,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s
 15. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))
 
 > **NB:** Quantification isn't performed if using `--aligner hisat2` due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.
+> **NB:** The `--aligner star_rsem` option will require STAR indices built from version 2.7.6a or later. However, in order to support legacy usage of genomes hosted on AWS iGenomes the `--aligner star_salmon` option requires indices built with STAR 2.6.1d or earlier. Please refer to this [issue](https://github.com/nf-core/rnaseq/issues/498) for further details.
 
 ## Quick Start