.gitignore

@@ -100,3 +100,12 @@ ENV/
 
 # Mac OS
 .DS_Store
+
+# nextflow analysis folders/files
+pipeline_trace*.txt*
+.nextflow*.log*
+report*.html*
+timeline*.html*
+/workflow/output/*
+/work/*
+/.nextflow/*

.gitlab-ci.yml

 before_script:
   - module add  python/3.6.1-2-anaconda
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
-  - module load  nextflow/0.31.0
+  - module load nextflow/0.31.0
   - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
 
 stages:
@@ -10,32 +10,37 @@ stages:
   - single
   - multiple
   - skip
+  - cleanup
 
 user_configuration:
   stage: unit
   script:
-  - pytest -m unit
   - pytest -m unit --cov=./workflow/scripts
 
+bash_tests:
+  stage: unit
+  script:
+    - module load singularity/3.0.2
+    - module load deeptools/2.5.0.1
+    - singularity run docker://bats/bats:v1.1.0 --tap workflow/tests/plot_profile.bats
+
 astrocyte:
   stage: astrocyte
   script:
-  - module load astrocyte/0.1.0
+  - module load astrocyte/0.3.1
   - module unload nextflow
   - cd ..
   - astrocyte_cli validate chipseq_analysis
-  artifacts:
-    expire_in: 2 days
+  after_script:
+    - rm -rf work/
 
 single_end_mouse:
   stage: single
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --astrocyte true -resume
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true --ci true --dev true
   - pytest -m singleend
-  artifacts:
-    expire_in: 2 days
 
 paired_end_human:
   stage: single
@@ -44,39 +49,55 @@ paired_end_human:
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false --ci true --dev true
   - pytest -m pairedend
-  artifacts:
-    expire_in: 2 days
 
-single_end_diff:
-  stage: multiple
+single_end_single_control:
+  stage: single
   only:
     - branches
   except:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false -resume
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false --ci true --dev true
+  - pytest -m singlecontrol
+
+single_end_diff:
+  stage: multiple
+  only:
+    - master
+  script:
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false --ci true --dev true
+  - pytest -m singleend
   - pytest -m singlediff
-  artifacts:
-    expire_in: 2 days
 
 paired_end_diff:
   only:
+    - branches
+  except:
     - master
   stage: multiple
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf --ci true --dev true
+  - pytest -m pairedend
   - pytest -m paireddiff
   artifacts:
-    expire_in: 2 days
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - flowchart.pdf
+    expire_in: 7 days
 
 single_end_skip:
   stage: skip
   only:
     - master
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --astrocyte false -resume
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false --ci true --dev true
   - pytest -m singleskip_true
-  artifacts:
-    expire_in: 2 days
+
+cleanup_job:
+  stage: cleanup
+  script:
+    - cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
+    - rm -fr $CI_PIPELINE_ID/

.gitlab/merge_request_templates/merge_request.md

 
-Please fill in the appropriate checklist below (delete whatever is not relevant). 
+Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 ## PR checklist
  - [ ] This comment contains a description of changes (with reason)
  - [ ] If you've fixed a bug or added code that should be tested, add tests!
  - [ ] Documentation in `docs` is updated
+ - [ ] Replace dag.png with the most recent CI pipleine integrated_pe artifact
  - [ ] `CHANGELOG.md` is updated
  - [ ] `README.md` is updated
-
+ - [ ] `LICENSE.md` is updated with new contributors

CHANGELOG.md

@@ -2,9 +2,46 @@
 
 All notable changes to this project will be documented in this file.
 
-## [Unreleased]
+## [publish_1.1.3 ] - 2020-08-16
+### Updated
+- Updated astrocyte to 0.3.1
 
-## [publish_1.0.4 ] - 2019-05-15
+### Fixed
+- Fixed missing gene names in annotation
+
+## [publish_1.1.2 ] - 2020-06-22
+- Add pipeline tracking
+
+## [publish_1.1.1 ] - 2020-04-23
+### Added
+- Add Nextflow to references.md
+- Add test data for test_pool_and_pseudoreplicate
+- Add PlotProfile Option
+- Add Python version to MultiQC
+- Add and Update tests
+- Use GTF files instead of TxDb and org libraries in Annotate Peaks
+- Make gtf and geneName files as param inputs
+- Add test data for single control and single replicate
+
+### Fixed
+- Fix references.md link in citation of README.md
+- Fix pool_and_psuedoreplicate.py to run single experiment
+- Fix xcor to increase file size for --random-source
+- Fix skip diff test for paired-end data
+- Fix xcor to get lowest non zero value above 50
+- Fix references to display in Multiqc report
+- Update astrocyte testing to 0.2.0
+
+## [publish_1.0.6 ] - 2019-05-31
+### Added
+- MIT LICENSE
+- Check for correct genome input
+- Check for correct output for motif serach
+
+### Fixed
+- Path to reference fasta file
+
+## [publish_1.0.5 ] - 2019-05-16
 ### Fixed
 - Retitled documentation for skipDiff and skipMotif to be more clear
 - Add missing python module for motif search

LICENSE.md

+MIT License
+
+Copyright (c) 2019, University of Texas Southwestern Medical Center.
+
+All rights reserved.
+
+Contributors: Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, Venkat S. Malladi
+
+Department: Bioinformatic Core Facility, Department of Bioinformatics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

-# **CHIPseq Manual**
-## Version 1.0.0
-## May 2, 2019
+# **ChIP-seq Manual**
+## Version 1.1.2
+## June 21, 2020
 
 # 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)
-[![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)
-[![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)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2648845.svg)](https://doi.org/10.5281/zenodo.2648845)
+|*master*|*dev*|
+|:-:|:-:|
+|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)|[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/dev/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/dev)|
+|[![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)|[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/dev/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/dev)|
+
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.31.0-brightgreen)](https://www.nextflow.io/)
+[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.3.1-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2648844.svg)](https://doi.org/10.5281/zenodo.2648844)
 
 
 ## 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 Department of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
+BICF ChIP-seq 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 Department 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://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-test.biohpc.swmed.edu/static/docs/index.html) using a simple web interface.
+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/chipseq_analysis
@@ -58,7 +60,10 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
       - --designFile '/path/to/file/design.txt',
       - --genome 'GRCm38', 'GRCh38', or 'GRCh37' (if you need to use another genome contact the [BICF](mailto:BICF@UTSouthwestern.edu))
       - --pairedEnd 'true' or 'false' (where 'true' is PE and 'false' is SE; default 'false')
-      - --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output (if not specficied will be under workflow/output/)
+      - --skipDiff 'true' or 'false' (where 'true' is skip differential peak and 'false' is do peak differential peak calling; default 'false')
+      - --skipMotif 'true' or 'false' (where 'true' is skip motif calling and 'false' is do motif calling; default 'false')
+      - --skipPlotProfile 'true' or 'false' (where 'true' is skip metageneplot for TSS and 'false' is do metageneplot for TSS; default 'false')
+      - --outDir (optional) path and folder name of the output data, example: /home2/s000000/Desktop/Chipseq_output (if not specified will be under workflow/output/)
 
 ## Pipeline
   + There are 11 steps to the pipeline
@@ -73,6 +78,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
     9. Annotate all peaks using ChipSeeker
     10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
     11. Use MEME-ChIP to find motifs in original peaks
+    12. Plot enrichment of signal around TSS
 
 See [FLOWCHART](docs/flowchart.pdf)
 
@@ -116,6 +122,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
 diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
 diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
 diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
+plotProfile | plotProfile.png | Plot profile of the TSS region
+plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
 
 ## Common Quality Control Metrics
   + These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
@@ -130,25 +138,25 @@ diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks
 If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know and we will add it here.
 
 ## Citation
-Please cite individual programs and versions used [HERE](docs/references.txt). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
+Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
 
 ## Programs and Versions
-  + python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.txt)
-  + trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.txt)
-  + cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.txt)
-  + bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.txt)
-  + samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.txt)
-  + sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.txt)
-  + bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.txt)
-  + deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.txt)
-  + phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.txt)
-  + macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.txt)
-  + UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.txt)
-  + R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.txt)
+  + python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.md)
+  + trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.md)
+  + cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.md)
+  + bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.md)
+  + samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.md)
+  + sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.md)
+  + bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.md)
+  + deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.md)
+  + phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.md)
+  + macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.md)
+  + UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.md)
+  + R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.md)
   + SPP/1.14
-  + meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.txt)
-  + ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.txt)
-  + DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.txt)
+  + meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.md)
+  + ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.md)
+  + DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.md)
 
 
 

astrocyte_pkg.yml

@@ -9,7 +9,7 @@
 # A unique identifier for the workflow package, text/underscores only
 name: 'chipseq_analysis_bicf'
 # Who wrote this?
-author: 'Holly Ruess, Spencer D. Barnes, Beibei Chen and Venkat Malladi'
+author: 'Holly Ruess, Spencer D. Barnes, Jeremy A. Mathews, Beibei Chen and Venkat Malladi'
 # A contact email address for questions
 email: 'bicf@utsouthwestern.edu'
 # A more informative title for the workflow package
@@ -52,6 +52,7 @@ workflow_modules:
   - 'R/3.3.2-gccmkl'
   - 'meme/4.11.1-gcc-openmpi'
   - 'pandoc/2.7'
+  - 'singularity/3.0.2'
 
 
 # A list of parameters used by the workflow, defining how to present them,
@@ -142,6 +143,15 @@ workflow_parameters:
     description: |
       Skip motif calling
 
+  - id: skipPlotProfile
+    type: select
+    required: true
+    choices:
+      - [ 'true', 'true']
+      - [ 'false', 'false']
+    description: |
+      Skip Plot Profile Analysis
+
   - id: astrocyte
     type: select
     choices:

docs/index.md

@@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste
     9. Annotate all peaks using ChipSeeker
     10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
     11. Use MEME-ChIP to find motifs in original peaks
+    12. Plot enrichment of signal around TSS
 
 
 ## Workflow Parameters
@@ -90,6 +91,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
 diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
 diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
 diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
+plotProfile | plotProfile.png | Plot profile of the TSS region
+plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
 
 ## Common Quality Control Metrics
   + These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
@@ -123,3 +126,6 @@ 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)

docs/references.md

@@ -49,9 +49,12 @@
   * Ross-Innes C. S., R. Stark, A. E. Teschendorff, K. A. Holmes, H. R. Ali, M. J. Dunning,  G. D. Brown, O. Gojis, I. O. Ellis, A. R. Green, S. Ali, S. Chin, C. Palmieri, C. Caldas, and J. S. Carroll. 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481: 389-393. doi:[10.1038/nature10730](https://dx.doi.org/10.1038/nature10730)
 
 16. **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)
+  * 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)
 
 17. **BICF ChIP-seq Analysis Workflow**:
-  * Spencer D. Barnes, Holly Ruess, Beibei Chen, & Venkat S. Malladi. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.4). Zenodo. doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844)
+  * Spencer D. Barnes, Holly Ruess, Jeremy A. Mathews, Beibei Chen, and Venkat S. Malladi. 2020. BICF ChIP-seq Analysis Workflow (publish_1.1.3). Zenodo. doi:[10.5281/zenodo.3986942](https://doi.org/10.5281/zenodo.3986942)
+
+18. **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)**.

docs/references.txt

-python/3.6.1-2-anaconda:
-Anaconda (Anaconda Software Distribution, https://anaconda.com)
-
-trimgalore/0.4.1:
-trimgalore/0.4.1 (https://github.com/FelixKrueger/TrimGalore)
-
-cutadapt/1.9.1:
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test_data/design_single_contol_SE.txt

+sample_id	experiment_id	biosample	factor	treatment	replicate	control_id	fastq_read1
+ENCLB497XZB	ENCSR000DXB	Panc1	H3K4me3	None	1	ENCLB304SBJ	ENCFF001GBW.fastq.gz
+ENCLB304SBJ	ENCSR000DXC	Panc1	Control	None	1	ENCLB304SBJ	ENCFF001HWJ.fastq.gz

test_data/fetch_test_data.sh

@@ -25,3 +25,9 @@ wget https://www.encodeproject.org/files/ENCFF161HBP/@@download/ENCFF161HBP.fast
 wget https://www.encodeproject.org/files/ENCFF776KZU/@@download/ENCFF776KZU.fastq.gz
 wget https://www.encodeproject.org/files/ENCFF119KHM/@@download/ENCFF119KHM.fastq.gz
 echo "Done with Paired-end"
+
+echo "Downloading Single-end data set Human ENCSR000DXB and ENCSR000DXC"
+wget https://www.encodeproject.org/files/ENCFF001GBW/@@download/ENCFF001GBW.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001GBV/@@download/ENCFF001GBV.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF001HWJ/@@download/ENCFF001HWJ.fastq.gz
+echo "Done with Single-end"

test_data/test_cross.qc

+Test.20.tagAlign.gz	18588987	0,20,33	0.211525291335199,0.211232019956852,0.211139666755398	35	0.2123067	1500	0.209429	1.01001	0.7284536       0