Resolve "Tests for astrocyte"

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• This comment contains a description of changes (with reason)
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Closes #39 (closed)

docs/index.md

-# 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/).
-