Update CHANGELOG.md and index.md

CHANGELOG.md

@@ -5,6 +5,7 @@ All notable changes to this project will be documented in this file.
 ## [Unreleased]
 - Fix references.md link in citation of README.md
 - Add Nextflow to references.md
+- Fix pool_and_psuedoreplicate.py to run single experiment
 
 ## [publish_1.0.6 ] - 2019-05-31
 ### Added

docs/index.md

@@ -123,3 +123,6 @@ Please cite in publications: Pipeline was developed by BICF from funding provide
   + meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)
   + ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)
   + DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)
+  + MultiQC [website](https://multiqc.info/) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)
+  + BICFChip-seqAnalysisWorkflow [website](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)
+  + Nextflow [website](https://www.nextflow.io/) [citation](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/references.md)