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@@ -4,16 +4,18 @@
 
 ### Pipeline updates
 
-* Added Salmon as an alternative method to STAR and HiSAT2
+* Added Salmon as an supplementary method to STAR and HiSAT2
+* Added `--psuedo_aligner`, `--transcript_fasta` and `--salmon_index` parameters
+* Add `Citation` and `Quick Start` section to `README.md`
+* Integrate changes in `nf-core/tools v1.6` template
 * Add tximport and summarizedexperiment dependency [#171](https://github.com/nf-core/rnaseq/issues/171)
+* Change all boolean parameters from snake_case to camelCase and vice versa for value parameters
 * Appointed changes because of missing output of the multiqc_plots folder [#200](https://github.com/nf-core/rnaseq/issues/200)
 * Add Qualimap dependency [#202](https://github.com/nf-core/rnaseq/issues/202)
 * Obtain edgeR + dupRadar version information [#198](https://github.com/nf-core/rnaseq/issues/198) and [#112](https://github.com/nf-core/rnaseq/issues/112)
 * Get MultiQC to save plots as [standalone files](https://github.com/nf-core/rnaseq/issues/183)
 * Get MultiQC to save plots as [standalone files](https://github.com/nf-core/rnaseq/issues/183): added the folder "multiqc_plots" to the output.
 * Get MultiQC to write out the software versions in a .csv file [#185](https://github.com/nf-core/rnaseq/issues/185)
-* Change all boolean parameters from snake_case to camelCase and vice versa for value parameters
-* Add `--skipSalmon` parameter to skip Salmon transcriptome quantification
 
 ### Dependency Updates