version-3.8.1

version-3.8.1
06/10/2026

DOCUMENTATION

• Update install procedure with link to utils/environment.yml #378
• Reference to geniac-template as been deleted. geniac-demo can serve as a template. #377

BUGFIX

• Fix a bug in definition files of recipes #381

version-3.8.0

version-3.8.0
05/27/2026

NEW FEATURES

• Nextflow code refactoring using workflows #352
• Ad-hoc variable to ensure reproducibility set in both assets/Dockerfile.env and assets/def.env #350
• New cmake options:
  • 'ap_docker_registry_push_repo' and 'ap_docker_registry_push_user' to push docker/podman container on a registry #351
  • 'ap_install_singularity_images_from_registry' to build apptainer sif file using docker/podman container available on a registry #351
  • 'ap_no_git' to deploy without git retrieving informations #366
• Update (auto-generation) data/cmake-init-default.cmake and documentation accordingly #358
• almalinux:9.7 set as default for the containers #361
• conda 26.1.1-3 from miniforge set as default for the containers #361
• Update apptainer version in conda env #360
• Remove files not used anymore #356
• Geniac CLI:
  • Check conda yml format in sections dependencies and pip #368
  • Check conda format in geniac.config #368
  • Python packaging:
    • Merge setup.cfg (setuptools) and pyproject.toml for python packages #364
    • Transfer cmake dependency from setup.cfg to conda env #364
  • Remove all Nextflow options from the geniac.ini file #369
  • Remove the checks in the linter relating to process scope options #369
    BUGFIX
• Get env name from yml conda file #353
• Update valid git tag pattern to handle production versions like v12.23.34 #359
• Remove gitlab-ci-token in the gitUrl label for container recipes (stepGitInfo.cmake) #362
• Replace pkg_resources (deprecated) by importlib.resources #349

DOCUMENTATION

• Update readthedocs config files (docs/environment.yml and .readthedocs.yml) #357
• Update the documentation with a "Contributing" section to detail how to develop geniac #355
• README file added to explain the content of each folder within the source code repository, inclusion of the README files within the rst file #355

version-3.7.0

version-3.7.0
05/23/2025

NEW FEATURES

• almalinux:9.5 set as default for the containers
• remove the use of the defaults conda channel to comply with anaconda license:
  • conda 24.11.3-2 from miniforge set as default for the containers
  • options '--condaNoDefaultsChannel' can to passed to nextflow to include the defaults conda channel in the yml files automatically generated by geniac
• git: geniac checks for production tage with patterns 'version-1.2.3' or 'v1.2.3'
• the geniac conda env does not use the defaults channel but the nodefaults channel
• Geniac CLI:
  • remove the use of the defaults conda channel to comply with anaconda license:
  • Check that the defaults channel is not used to comply with anaconda license
  • option 'condaNoDefaultsChannel' in geniac.ini file allows the use of the defaults conda channel if needeed

version-3.6.0

version-3.6.0
01/10/2025

NEW FEATURES

• Geniac CLI:
  • Environment variables from the user space are passed to the sudo command
  • Conda env with nextflow 24.04.4, pip 24.2, make 4.4.1, python 3.12.5
  • geniac must be installed using pip after the geniac conda env is created

BUGFIX

• Geniac CLI:
  • Both ADD and COPY directives in Dockerfile are considered to check file dependencies

version-3.5.0

version-3.5.0
08/27/2024

NEW FEATURES

• a sha256sum signature is generated for each container recipe (including its dependencies). The list of signatures is provided both as global file (sha256sum) and individual files for each tool (eg python.sha256sum)
• new cmake option 'ap_container_list' to build only a subset of container provided as a list in a txt file.

version-3.4.0

version-3.4.0
08/08/2024

NEW FEATURES

• nextflow scripts have been migrated to DSL2
• Geniac CLI:
  • Return exit code 1 on any error with the CLI.

version-3.3.0

version-3.3.0
04/12/2024

NEW FEATURES

• almalinux:9.3 set as default for the containers
• conda 23.10.0 set as default for the containers

version-3.2.1

version-3.2.1
10/12/2023

BUGFIX

• singularity/docker profiles:
  • post commands were written twice in the recipes generated by geniac

version-3.2.0

version-3.2.0
09/08/2023

NEW FEATURES

• singularity/docker profiles:
  • params.yumOptions added ine the nextflow.config file, and options set with '--setopt=fastestmirror=1 --setopt=metadata_expire=0'
• new profile created by geniac: apptainer (since 'apptainer.enabled' has been introduced in nextflow 23.04.0)
• Geniac CLI:
  • 'geniac lint': consider that the nextflow pipeline is implemented using DSL2. Modifications have been made only for process using renv. 'geniac lint' could still work on DSL1 pipeline provided that there is no process using renv.
  • Update conda env with new tool versions

version-3.1.0

version-3.1.0
08/14/2023

NEW FEATURES

• almalinux:8.8 set as default for the containers
• conda 25.3.1 set as default for the containers
• micromamba is used to create conda envs and install conda packages
• conda/multiconda profiles:
  • conda.enable has been added
• Geniac CLI:
  • Conda env with apptainer 1.2.2, nextflow 22.10.6, pip 23.2.1