Update readme and add in coverage.

.gitlab-ci.yml

 before_script:
   - module add  python/3.6.1-2-anaconda
-  - pip install --user pytest-pythonpath
+  - pip install --user pytest-pythonpath pytest-cov
   - module load nextflow/0.24.1-SNAPSHOT
   - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
 
@@ -18,8 +18,9 @@ single_end_mouse:
   script:
   - nextflow run workflow/main.nf
   - pytest -m integration
+  - pytest --cov=./workflow/scripts 
 
 paired_end_human:
   stage: integration
   script:
-  - nextflow run workflow/main.nf --designFile "test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'
+  - nextflow run workflow/main.nf --designFile "$baseDir/../test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'

README.md

+# BICF ChIP-seq Pipeline
+
+[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
+)](https://www.nextflow.io/)
+[![Coverage Report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
+
+
+## Introduction
+BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Dept. of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
+
+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://biohpc.swmed.edu/). However, the pipeline should be able to run on any system that Nextflow supports.