Merge pull request #83 from databio/dev

Update to 0.8.5

.github/issue_template.md

@@ -0,0 +1 @@
+<!-- If applicable, please attach the entire PEPATAC_log.md file from your failed run. This includes information about versions that will help us diagnose your problem. -->

.gitignore

@@ -5,7 +5,11 @@
 # Tests
 .cache/
 
+# MkDocs files
+site/
+
 # Jekyll files
+jekyll/
 _site
 .DS_store
 .jekyll

CHANGELOG.md

@@ -1,6 +1,14 @@
 # Change log
 All notable changes to this project will be documented in this file.
 
+## [0.8.5] -- 2019-03-19
+
+### Changed
+- Convert and update documentation
+- Fixed a bug with feature naming
+- Improve bamSitesToWig modularity
+- Move large files to separate host site
+
 ## [0.8.4] -- 2019-01-03
 
 ### Changed
@@ -143,3 +151,4 @@ All notable changes to this project will be documented in this file.
 ## [0.1.0]
 ### Added
 - First release of ATAC-seq pypiper pipeline
+

README.md

@@ -1,9 +1,27 @@
-<a href="http://pepkit.github.io"><img src="http://pepkit.github.io/img/PEP-compatible-green.svg" alt="PEP compatible" style="float:left; margin:10px"></a>
+<img src="docs/img/pepatac_logo_white.svg" alt="pepatac logo" height="70" align="left"/>
 
-# PEPATAC
+<br></br>
+
+---
+
+[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
 PEPATAC is a pipeline designed to process ATAC-seq data. For more information see: http://code.databio.org/PEPATAC/
 
+## Docs
+
+Develop docs with:
+
+```
+mkdocs serve -f mkdocs.yml
+```
+
+Build and deploy with:
+
+```
+mkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/caravel/
+```
+
 ## Contributing
 
 Pull requests welcome. Active development should occur in a development or feature branch.
@@ -16,3 +34,4 @@ Pull requests welcome. Active development should occur in a development or featu
 * Ryan Corces, [email protected]
 * Vince Reuter, [email protected]
 * Others... (add your name)
+

anno/README.md

@@ -0,0 +1,7 @@
+<img src="../docs/img/pepatac_logo_white.svg" alt="pepatac logo" height="70" align="left"/>
+
+<br></br>
+
+---
+
+Place a [pre-built downloadable genome annotation file](http://big.databio.org/pepatac/) in this directory, or read the [guide to create your own](http://code.databio.org/PEPATAC/howto/create-annotation-file/).

docs/README.md

@@ -1,21 +1,35 @@
-# [PEPATAC documentation](http://code.databio.org/PEPATAC)
+# <img src="img/pepatac_logo_black.svg" alt="PEPATAC" class="img-fluid" style="max-height:60px; margin-top:10px; margin-bottom:-10px" align="left">  
 
-This repository is viewable at [code.databio.org/PEPATAC](http://code.databio.org/PEPATAC). It holds HTML documentation for the PEPATAC pipeline.
+<br clear="all">
 
-## Building PEPATAC documentation with jekyll:
+[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
-`jekyll build pepatac`
+`PEPATAC` is an ATAC-seq pipeline for ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches. It performs adapter trimming, mapping, peak calling, and creates bigwig tracks, TSS enrichment files, and other outputs. 
 
-## Do it with `docker` or `singularity`!
+## Outputs
 
-1. Grab the container
+`PEPATAC` produces quality control plots, summary statistics, and several data formats to set the stage for project-specific analysis. 
 
-   `docker pull nsheff/jim`   
-   *or*  
-   `singularity build jim docker://nsheff/jim`
+- PEPATAC produces an HTML report: View this [HTML Summary report demo](files/examples/gold/summary.html)
+- We have produced an [interactive display of the output folder structure](browse_output/), which includes:
+	- [Easily parsable summary statistics file](files/examples/gold/results_pipeline/gold5/stats.tsv)
+	- Called peaks (in both `narrowPeak` and `bigBed` format)
+	- BigWig signal tracks:
+	    - nucleotide-resolution ("exact cut") signal
+	    - smoothed signal
+	- Plots:               
+	    - [TSS enrichment plot](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_TssEnrichment.pdf)
+	    - [TSS distance distribution](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_peaks_TSS_dist.pdf)
+	    - [Fragment length distribution](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_fragLenDistribution.pdf)
+	    - [Peak chromosomal distribution](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_peaks_chr_dist.pdf)
+	    - [Peak genomic partition distribution](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_peaks_partition_dist.pdf)
+	    - [Fraction of reads *and/or* peaks in features (FRiF)](files/examples/gold/results_pipeline/gold5/QC_hg19/gold5_frif.pdf)
 
-2. Build the website
 
-   `docker run jim jekyll build pepatac`  
-   *or*  
-   `singularity exec jim jekyll build pepatac`
+## User interface
+
+`PEPATAC` is a python script that runs on the command line (See [usage](usage)). It can also read projects in [PEP format](https://pepkit.github.io/). This means that `PEPATAC` projects are also compatible with other PEP tools, and output can be convenient read into `R` using [the `pepr` package](http://code.databio.org/pepr/) or into `Python` using the [`peppy` package](https://peppy.readthedocs.io/en/latest/). The pipeline itself is customizable, enabling a user to adjust individual command settings or even swap out specific software by editing a few lines of human readable configuration files.
+
+## Availability
+
+You can download the latest version from the [releases](https://github.com/databio/pepatac/releases) page, or find changes listed in the [CHANGELOG](changelog).