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

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

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## [0.4.0] - 2019-11-18
### Added
- Add new tools (star,...)
- conda support at the psmn

## Changed
- configuration simplification
- docker and singularity image download instead of local build
- hidden directories in `src` for project clarity (only `nf_modules` is visible)

## Removed
- conda support at in2p3 with `-profile in2p3_conda`

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## [0.3.0] - 2019-05-23
### Added
- Add new tools (umi_tools, fastp,...)
- singularity support at in2p3 with `-profile in2p3`
- conda support at in2p3 with `-profile in2p3_conda`

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## [0.2.9] - 2019-03-26
### Added
- Add new tools (fastq, macs2, umitools, ...)
- singularity support

### Changed
- every tool name is now in lowercase in each module section

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## [0.2.7] - 2018-10-23
### Added
- Add new tools (BWA, GATK, sambamba, ...)

### Changed
- `sge` profile is now called `psmn` profile to prepare tests in the CCIN2P3
- every `psmn` config file has an update configuration for mono or 16 cpus queues
- update process naming to follow new nextflow format

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## [0.2.6] - 2018-08-23
### Added
- Added `src/training_dataset.nf` to build a small training dataset from NGS data
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### Changed
- the structure of `src/nf_modules`: the `tests` folder was removed

## [0.2.5] - 2018-08-22
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### Added
- This fine changelog

### Changed
- the structure of `src/nf_modules`: the `tests` folder was removed

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## [0.2.4] - 2018-08-02
### Changed
- add `paired_id` variable in the output of every single-end data processes to match the paired output


## [0.2.3] - 2018-07-25
### Added
- List of tools available as nextflow, docker or sge module to the `README.md`


## [0.2.2] - 2018-07-23
### Added
- SRA module from cigogne/nextflow-master 52b510e48daa1fb7


## [0.2.1] - 2018-07-23
### Added
- List of tools available as nextflow, docker or sge module


## [0.2.0] - 2018-06-18
### Added
- `doc/TP_computational_biologists.md`
- Kallisto/0.44.0

### Changed
- add `paired_id` variable in the output of every paired data processes
- BEDtools: fixes for fasta handling
- UrQt: fix git version in Docker


## [0.1.2] - 2018-06-18
### Added
- `doc/tp_experimental_biologist.md` and Makefile to build the pdf
- tests files for BEDtools

### Changed
- Kallisto: various fixes
- UrQt: improve output and various fixes

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### Removed
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- `src/nf_test.config` modules have their own `.config`


## [0.1.2] - 2018-06-18
### Added
- `doc/tp_experimental_biologist.md` and Makefile to build the pdf
- tests files for BEDtools

### Changed
- Kallisto: various fixes
- UrQt: improve output and various fixes

### Removed
- `src/nf_test.config` modules have their own `.config`


## [0.1.0] - 2018-05-06
This is the first working version of the repository as a nextflow module repository