diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 66e1fd4a0cf9d2c584c4efaceeeec5cc3f47384a..f69a33854b99af4b0332ebb2885cbe74e502ab52 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,14 +6,24 @@ before_script:
 
 stages:
   - unit
+  - astrocyte
   - integration
 
 user_configuration:
   stage: unit
   script:
-  - pytest -m unit
   - pytest -m unit --cov=./workflow/scripts
 
+
+astrocyte:
+  stage: astrocyte
+  script:
+  - module load astrocyte/0.3.0
+  - module unload nextflow
+  - cd ..
+  - astrocyte_cli validate atacseq_analysis
+
+
 single_end_human:
   stage: integration
   only:
diff --git a/README.md b/README.md
index 42ebb3ae3e154553740da378c43cd9e512f8a3d0..e728031e0d6d298751b0d195eeafe81efad37360 100644
--- a/README.md
+++ b/README.md
@@ -25,11 +25,11 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
 ```
 
 ## Input files
-##### 1) Fastq Files
+### Fastq Files
   + You will need the full path to the files for the Bash Scipt
 
 
-## Design file
+### Design file
   + The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End.  Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:
 
     1. sample_id - The id of the sample. This will be the header in output files, please make sure it is concise
@@ -37,7 +37,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
     3. replicate - Replicate number
     4. fastq_read1 - Name of fastq file 1 for SE or PE data
     5. fastq_read2 - Name of fastq file 2 for PE data
-    
+
   + See [HERE](/docs/design_ENCSR451NAE_PE.txt) for an example design file, paired-end
   + See [HERE](/docs/design_ENCSR265ZXX_SE.txt) for an example design file, single-end
 
@@ -112,9 +112,8 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
 
 
 ## Citation
-Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi: coming soon. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
+Please cite individual programs and versions of pipeline used [HERE](docs/references.md), and the overall pipeline doi: 10.5281/zenodo.3526149. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
 
 
 ### Credits
 This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
-
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index b031e84e2e43a04f29c6a43d01dd675d22ce85d5..e60e5f07e5d8b78a17e38ceb91710f47f80c35bd 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -46,12 +46,12 @@ workflow_modules:
   - 'bwa/intel/0.7.12'
   - 'samtools/1.4.1'
   - 'sambamba/0.6.6'
-  - 'bedtools/2.26.0'
+  - 'bedtools/2.25.0'
   - 'deeptools/2.5.0.1'
   - 'phantompeakqualtools/1.2'
   - 'macs/2.1.0-20151222'
   - 'UCSC_userApps/v317'
-  - 'singularity/2.6.1'
+  - 'R/3.3.2-gccmkl'
   - 'pandoc/2.7'
   - 'singularity/3.0.2'
 
@@ -95,7 +95,7 @@ workflow_parameters:
     description: |
       One or more input FASTQ files from a ATAC-seq expereiment and a design
       file with the link bewetwen the same file name and sample id
-    regex: ".*(fastq|fq)*"
+    regex: ".*(fastq|fq)*gz"
 
   - id: pairedEnd
     type: select
@@ -117,7 +117,7 @@ workflow_parameters:
       - [ 'true', 'True']
       - [ 'false', 'False']
     description: |
-      The Blacklisted Regions aim to identify a comprehensive set of regions 
+      The Blacklisted Regions aim to identify a comprehensive set of regions
       that have anomalous, unstructured, high signal/read counts in next gen
       sequencing experiments independent of cell line and type of experiment.
       If you would like these regions excluded from replicated peaks, select
@@ -134,12 +134,22 @@ workflow_parameters:
     type: select
     choices:
       - [ 'GRCh38', 'Human GRCh38']
-      - [ 'GRCh38', 'Mouse GRCh38']
+      - [ 'GRCm38', 'Mouse GRCm38']
     required: true
     description: |
       Reference species and genome used for alignment and subsequent analysis.
 
 
+  - id: astrocyte
+    type: select
+    choices:
+      - [ 'true', 'true' ]
+    required: true
+    default: 'true'
+    description: |
+      Ensure configuraton for astrocyte.
+
+
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------
@@ -148,7 +158,7 @@ workflow_parameters:
 #            The workflow must publish all final output into $baseDir
 
 # Name of the R module that the vizapp will run against
-vizapp_r_module: 'R/3.2.1-intel'
+vizapp_r_module: 'R/3.4.1-gccmkl'
 
 # List of any CRAN packages, not provided by the modules, that must be made
 # available to the vizapp
@@ -158,8 +168,4 @@ vizapp_cran_packages:
 
 # List of any Bioconductor packages, not provided by the modules,
 # that must be made available to the vizapp
-vizapp_bioc_packages:
-#  - qusage
-#  - ballgown
-vizapp_github_packages:
-  - js229/Vennerable
+vizapp_bioc_packages: []
diff --git a/docs/index.md b/docs/index.md
index 42ebb3ae3e154553740da378c43cd9e512f8a3d0..2b881aa227a43faf545a78213a68ec9f55eb338f 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,10 +1,4 @@
-# Astrocyte ATAC-seq analysis Workflow Package
-
-[![pipeline Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
-[![Coverage Report](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/commits/master)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
-)](https://www.nextflow.io/)
-[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+# BICF ATAC-seq Analysis Workflow
 
 
 ## Introduction
@@ -12,22 +6,10 @@ BICF ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-
 
 The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
 
-This pipeline is primarily used with a SLURM cluster on the [BioHPC Cluster](https://portal.biohpc.swmed.edu/content/). However, the pipeline should be able to run on any system that supports Nextflow.
-
-Additionally, the pipeline is designed to work with [Astrocyte Workflow System](https://astrocyte.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
-
-Current version of the software and issue reports are at
-https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis
-
-To download the current (working not tagged) version of the software
-```bash
-$ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
-```
 
 ## Input files
 ##### 1) Fastq Files
-  + You will need the full path to the files for the Bash Scipt
-
+  + One or more input FASTQ files from a ATAC-seq experiment
 
 ## Design file
   + The Design file is a tab-delimited file with 4 columns for Single-End and 5 columns for Paired-End.  Letter, numbers, and underlines can be used in the names. However, the names must begin with a letter. Columns must be as follows:
@@ -37,7 +19,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/atacseq_analysis.git
     3. replicate - Replicate number
     4. fastq_read1 - Name of fastq file 1 for SE or PE data
     5. fastq_read2 - Name of fastq file 2 for PE data
-    
+
   + See [HERE](/docs/design_ENCSR451NAE_PE.txt) for an example design file, paired-end
   + See [HERE](/docs/design_ENCSR265ZXX_SE.txt) for an example design file, single-end
 
@@ -112,9 +94,8 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
 
 
 ## Citation
-Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi: coming soon. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
+Please cite individual programs and versions of pipeline used [HERE](docs/references.md), and the overall pipeline doi: 10.5281/zenodo.3526149. Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
 
 
 ### Credits
 This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
-
diff --git a/docs/references.md b/docs/references.md
index 34656dbf5dd5873aec671d436d2eabd5fc236e13..0ef24b27fd70a18cb9b648e575cdc0f28ff663ad 100644
--- a/docs/references.md
+++ b/docs/references.md
@@ -40,7 +40,11 @@
 13. **MultiQc**:
   * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
 
-14. **Nextflow**:
+
+14. **BICF ChIP-seq Analysis Workflow**:
+  *  Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.0). Zenodo. doi:[10.5281/zenodo.3891417](https://doi.org/10.5281/zenodo.3891417)
+
+15. **Nextflow**:
   * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.
 
 Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 8472bf6b235c1b27c71473a027cda61dcf4fec10..1a20d57547cef8f65929dccbf3ae51e87187fbf2 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -50,7 +50,7 @@ process {
     executor = 'local'
   }
   withName: experimentQC {
-    module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1', 'samtools/1.4.1', 'bedtools/2.25.0', 'singularity/2.6.1']
+    module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1', 'samtools/1.4.1', 'bedtools/2.25.0', 'singularity/3.0.2'']
     queue = '128GB,256GB,256GBv1'
   }
   withName: multiqcReport {