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

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## [1.2.0] - 28th april 2020
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### Added

* copy and rename files generated from results/18_table_assigned_sequences/ to results/ folder
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* `scripts/cat_samples_into_runs.sh` bash script to merge {sample} files into {projmarkrun} file
* custom reference database taxonomic assignment rules
* custom reference base taxonomic assignment config parameters
* `scripts/link_custom_runs` bash script to duplicate as symlink each {projet}/{marker}/{run} analysis in order to process parallel analysis on custom reference database in addition to the ncbi reference database
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### Changed

* all worklows are merged into a single one
* results subfolders are generated automatically
* unique scripts, rules and envs folders
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* Fix SettingWithCopyWarning pandas dataframe
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### Removed

* old folders and scripts 01_settings, 02_assembly, 03_demultiplex, etc...
* old preexisting subfolders into results folder
* clean.sh script which is now useless
* rename.sh script which is replaced by a rule in Snakefile


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## [1.1.4] - 16th september 2020
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### Added

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* can handle 2 different types of input format CLASSIC and RAPIDRUN
* tutorial to process data in CLASSIC format based on a subset of Rhone project data

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### Changed

* rapidrun all_samples.tsv replaced by all_samples.csv with `;` as separator

### Removed

* Unuseful or deprecated config files


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## [1.1.3] - 27th july 2020
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### Added
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* tutorial commands and folders
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* tutorial configuration file
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* clean.sh a script to remove intermediate files, log files and final results files
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### Changed

* main.sh launches whole workflow
* fix tutorial commands


## [1.1.2] - 21st july 2020
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### Added

* multithreaded assembly step for large fastq files

### Changed

* fix main.sh so it can run into a single command

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### Removed

* picture of DAG files

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## [1.1.1] - 3rd july 2020
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### Added

* Tutorial
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* Documentation
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* gitignore
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* Autorship
* license MIT
* Singularity/Docker recipe for obitools
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## [1.1.0] - 22th june 2020
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### Added

* data test
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* Conda v4.8.2 envs

### Changed

* upgrade snakemake to v5.19.2
* new structure for distribution based on snakemake recommandation [here](https://snakemake.readthedocs.io/en/v5.19.2/snakefiles/deployment.html)

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### Removed

* infos folder


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## [1.0.1] - 14th june 2020

### Changed
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* Absolute path of all_samples.tsv into config.yaml
* Remove redundant paramters into config.yaml
* Fix name of count parameters into filter_samples.smk
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## [1.0.0] - 25th may 2020

### Added
 
* Complete workflow
* snakemake rule system to handle rapidrun files

### Changed

* upgrade singularity to v3.6

### Removed

* marker.csv