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# Changelog

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

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## [publish_1.1.3 ] - 2020-08-16
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### Updated
- Updated astrocyte to 0.3.1

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### Fixed
- Fixed missing gene names in annotation

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## [publish_1.1.2 ] - 2020-06-22
- Add pipeline tracking

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## [publish_1.1.1 ] - 2020-04-23
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### Added
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- Add Nextflow to references.md
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- Add test data for test_pool_and_pseudoreplicate
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- Add PlotProfile Option
- Add Python version to MultiQC
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- Add and Update tests
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- Use GTF files instead of TxDb and org libraries in Annotate Peaks
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- Make gtf and geneName files as param inputs
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- 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
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- Fix xcor to increase file size for --random-source
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- Fix skip diff test for paired-end data
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- Fix xcor to get lowest non zero value above 50
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- Fix references to display in Multiqc report
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- Update astrocyte testing to 0.2.0
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## [publish_1.0.6 ] - 2019-05-31
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### Added
- MIT LICENSE
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- Check for correct genome input
- Check for correct output for motif serach

### Fixed
- Path to reference fasta file
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## [publish_1.0.5 ] - 2019-05-16
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### 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