CHANGELOG.md

Changelog

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.

[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

[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

[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

[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

[0.2.6] - 2018-08-23

Added

• Added src/training_dataset.nf to build a small training dataset from NGS data

Changed

• the structure of src/nf_modules: the tests folder was removed

[0.2.5] - 2018-08-22

Added

• This fine changelog

Changed

• the structure of src/nf_modules: the tests folder was removed

[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

Removed

• 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