@@ -19,8 +19,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Deprecated`
* --skipMaps, --skipIce, --skipCool, --skipMultiQC are deprecated and replaced by --skip_maps, --skip_ice, --skip_cool, --skip_multiqc
* --saveReference, --saveAlignedIntermediates, --saveInteractionBAM are replaced by --save_reference, --save_aligned_intermediates, --save_interaction_bam