All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
v1.0.0 - Aztekium, 05-05-2024
- Added PA filters to keep peaks at less or more than 10 or 100 kilobases (lt10kb, lt100kb, mt10kb, mt100kb). #22, 021de6f
- Added PA filters to keep peaks at less than arbitrary defined cutoffs (ltXkb, mtYkb), with cutoffs defined with the new parameters custom_distance__less_than_X_b and custom_distance__more_than_Y_b. #22, 021de6f
- Fixed a small typo that was making the previous release (0.9.0) crash during the DA_ATAC__saving_detailed_results_tables process. #21, 5ac9710, 827df11
- Removed the PA filters: 3kb, 8kb, and 30kb. #22
v0.9.0 - Gymnocalycium, 22-04-2024
- Added a tutorial section in the documentation and an associated script. #20
- Added figures for the manuscript: genome track plots, examples of figures and tables from the worm test dataset. #20
- Added Peak Annotation filters to keep only peaks at less than 3, 8 or 30 kilobases to their closest gene. #20, 8ab3377
- Added ChIPseeker options to ignore upstream or downstream of peak for closest gene annotation. #20, 7f797f8
- Added quickstart scripts. #19
- Fixing a typo which prevented bigWig files from being saved. #20, 250afb6
v0.8.6 - Pygmaeocereus, 30-11-2023
- Added the code for the case study. #18
v0.8.5 - Harrisia, 28-11-2023
- Changed the code to make Cactus work with the latest versions of Singularity, Docker, conda and Mamba. c875799
- Changed the documentation of the Quickstart and dependencies. 567e048 f8b2027
- Changed the documentation of the new containers. e89cb32
- Changed the Nextflow version manifest to give an error message if a wrong version is used. 51981f3
- Fixed the conda and mamba bugs from the previous release by creating new mulled containers. c875799 6cfcf16
- Fixed bugs to run the main.nf and the download.nf scripts with Docker. 716adc2 c947936
- Upgraded dependencies: Docker 24.0.5, build 24.0.5-0ubuntu1~20.04., conda: 23.7.4, Mamba: 1.4.2. 567e048
v0.8.4 - Matucana, 09-06-2023
- Changed the code to make Cactus work with the latest versions of Nextflow, Singularity and Docker. ce2b6dd
- Changed the documentation to clarify the dependencies. 0f45173
- Changed the CITATIONS.md and the README.md to add a link to Cactus preprint. 0e7b6ba
- Fixed a bug happening in conda/Mamba when users have a .Renviron or a .Rprofile file. a188dbb
- Fixed a bug with conda/Mamba for merging pdf. a188dbb
- Deprecated the use of conda and Mamba temporarily until a bug in conda is resolved. 0f45173
v0.8.3 - Espostoopsis, 15-05-2023
- Fixed a bug in the heatmap process that made the fly test dataset fail. #11
v0.8.2 - Mammilloydia, 12-05-2023
- Added options to keep unique DA and NDA genes or not in the splitting process. #6
- Changed the docs. #5
- Fixed a bug in the script to download test datasets and references. #8
v0.8.1 - Cephalocereus, 19-04-2023
- Added a functionality to manually set the size of the numbers indicating the overlap in the cells for the heatmap figures. bf0f8aa
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Changed the docs to match with latest version of manuscript in preparation. bc11d3a, ac0eafa, f273951, cf934e2, 285d579, f04cd11, f68018b, 37ad16c
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Changed labels in the heatmap to improve clarity. 1fd6d20
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Fixed bugs in the heatmap process. eb3de68
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Fixed a bug with the plot_FDR_by_PA_filters function. 4e5cafc
v0.8.0 - Lophophora, 30-12-2022
First release.