# Changelog

All notable changes to this project will be documented in this file.

## [Unreleased]
### Updated
- Updated astrocyte to 0.3.1

## [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
- Updated links for phantompeaktools and references
- Fix callPeaks for single control experiments

## [publish_1.0.3 ] - 2019-04-23
### Fixed
- Variable name for design file for Astrocyte
- File path for design file to work for Astrocyte

## [publish_1.0.0 ] - 2019-04-23
Initial release of pipeline