Package: geniac
GeniacGeniacis anAutomaticConfigurationGENerator andInstaller for nextflow pipelines.DocumentationAcknowledgementsRelease notesCitationDocumentationThegeniac documentationprovides a set of best practises to implementNextflowpipelines.Thegeniacsource code provides the set of utilities.Thegeniac demoprovides a toy pipeline to test and practiseGeniac.Thegeniac demo DSL2provides a toy pipeline to test and practiseGeniacwithNextflowDSL2.Thegeniac templateprovides a pipeline template to start a new pipeline.AcknowledgementsInstitut CurieCentre national de la recherche scientifiqueThis project has received funding from the European Union’s Horizon 2020 research and innovation programme and the Canadian Institutes of Health Research under the grant agreement No 825835 in the framework on theEuropean-Canadian Cancer NetworkCitationAllain F, Roméjon J, La Rosa P et al. Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines. Open Research Europe 2021, 1:76version-3.2.1
10/12/2023BUGFIXsingularity/docker profiles:post commands were written twice in the recipes generated by geniacversion-3.2.0
09/08/2023NEW FEATURESsingularity/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 versionsversion-3.1.0
08/14/2023NEW FEATURESalmalinux:8.8 set as default for the containersconda 25.3.1 set as default for the containersmicromamba is used to create conda envs and install conda packagesconda/multiconda profiles:conda.enable has been addedGeniac CLI:Conda env with apptainer 1.2.2, nextflow 22.10.6, pip 23.2.1DOCUMENTATIONrenv updated with BioC 3.17version-3.0.0
05/05/2023NEW FEATURESsingularity profile:the profile has been simplified since the option '--containall' has been removed and the profile now sets 'autoMounts = true'functionalities introduced in version 2.6.* to manage singularity bindings are not needed anymoreoption 'params.containers.specificBinds' (used in the geniac-template) introduced in version-2.1.0 is not needed anymorecmake option 'ap_mount_dir' introduced in version-2.0.0 to bind folders inside containers is now deprecated since it is not needed anymorePossibility to define label with variable: label (params.someValue ?: 'toolPrefix')Geniac CLI:'geniac lint': improve error message when name of a conda recipe is not coherent with the labelversion-2.6.3
01/06/2023NEW FEATURESsingularity profile:Allow the binding of relative (to launchDir) pathsOrder the bindings according to the natural orderingGeniac CLI:Possibility to use 'geniac lint' on a repo even if the folder "geniac" is not present'geniac init':  improve error message displayDOCUMENTATIONGit clone using geniac submodule from remote release branchBUGFIXGeniac CLI:Avoid to launch Cmake init on several geniac CLI commands'geniac options': display missing optionsversion-2.6.2
12/16/2022NEW FEATURESGeniac CLI:Conda env with apptainer 1.1.4BUGFIXsingularity profile:checkSymlink: avoid infinite loop in some limit conditionsversion-2.6.1
12/07/2022BUGFIXsingularity profile:checkSamplePlan: conditions added to consider files with either 2, 3 or 4 columnsversion-2.6.0
11/19/2022NEW FEATURESalmalinux:8.7 set as default for the containerssingularity profile:checkBindinds function takes into account the binding of possible symlink inside a path. It also binds the directory defined in 'params.outDir' if it is defined in the nextflow.config file.BUGFIXGeniac CLI:'geniac init' will throw an error if it is launched from the working directory to be createdversion-2.5.0
08/04/2022NEW FEATURESAdd support to apptainerUpgrade tool versions for the geniac conda envCheck during the cmake configuration that mininal version for each software is metGeniac CLI:geniac lint adds an error message if conda recipe is not correctly formattedgeniac lint will ignore config file that are not explicitly declared in geniac.iniwhen installing with sudo privilege, check that singularity and nextflow versions are the same as the one detected in the user environment during cmake configurationavoid 'sudo' command with 'geniac install' if launched by the root userBUGFIXGeniac CLI:Fix geniac lint error when comment in the middle of a linegeniac lint will throw an error if the withLabel process selector is single-line formatted in the process.config fileallow '.' in softName in the pip section of a conda recipeDOCUMENTATIONMinimal conda version (4.12.0) requiredversion-2.4.1
06/10/2022NEW FEATURESGeniac CLI:allow both patterns ('condaChannelName::softName=version=buildString' and 'softName=version=buildString') in conda yml recipe fileversion-2.4.0
06/08/2022NEW FEATURESconda 4.12.0 and almalinux:8.6 set as default for the containersGeniac CLI:check that conda recipe with a yml file contains an env namecheck that conda recipe with a yml file have a unique env namecheck that all dependencies with conda follow the pattern 'condaChannelName::softName=version=buildString'check that pip dependencies with conda follow the pattern 'softName==version'DOCUMENTATIONGuidelines to write conda recipe with a yml fileversion-2.3.0
05/20/2022NEW FEATURESNew cmake option:ap_singularity_build_options: allow to pass specific options when building singularity images.Geniac CLI:singularityfakeroot mode added to "geniac install"default runOption expected to "" in geniac.configNew profile available: podmanBUGFIXDelete files generated by geniac when "geniac init" uses a pathDOCUMENTATIONDescribe how to build singularity images with fakeroot optionAdmin: explain how to build the docversion-2.2.0
04/27/2022NEW FEATURESgenerate container recipes with renv and R toolconda 4.11.0 and almalinux:8.5 set as default for the containersGeniac CLI:"clean", "configs" and "recipes" commands have been addedallow labels defined in params.geniac.tools in conf/geniac.config to use the content from other tools defined in params.geniac.toolsallow labels in params.geniac.containers.yum or params.geniac.containers.git scopes for all kind of labels (and not only for labels defined in params.geniac.tools)check that the container recipes generated by geniac are not in the repoallow custom scope in params.geniac.tools (which is required for a tool with R and renv)geniac folder with the same version of geniac CLI is now included in the python packageadd "sudo chown" after sudo operation to restore permission to the user"geniac lint" now checks that a conda recipe must have its label in conf/geniac.configDOCUMENTATIONNew section with the Geniac CLI commandsExplain how to add a process with R and renv to manage package dependenciesBUGFIX:Geniac CLI:change regex to check that a module fromSource is in the ExternalProject_Add directiveversion-2.1.0
03/24/2022NEW FEATURESGeniac CLI:geniac folder with the same version of geniac CLI is downloaded in src dir to ensure that the pipeline will be installed using the same geniac versionconfig files generated by geniac are deleted at init if they are present in the src dirDOCUMENTATIONoption containers.specificBindsversion-2.0.1
03/18/2022DOCUMENTATIONUpdate the config file examples generated by geniacBUGFIXGeniac CLI: allow the usage of --ap_singularity_image_pathversion-2.0.0
02/10/2022NEW FEATURESTools from source:they are installed in ${projectDir}/bin/fromSource in order to allow their usage inside the containersthe sh script which allowed the installation inside the container is not needed anymoreallow multi-stage building when building docker containersTools with custom install:their dependencies files needed to build the containers have to be located in recipes/dependencies/label_name (to allow the -resume option)New cmake options:ap_linux_distro and ap_conda_release to bootstrap on containers available on 4geniac docker hub repositories (https://hub.docker.com/u/4geniac)ap_mount_dir to bind folders inside containerssingularity profile:'autoMounts = false' when nextflow launches singularity profilecheckBindinds function added in singularity.config to avoid any interaction with HOME of the host for better reproducibilityimage extension is now '.sif' instead of '.simg'singularity/docker profile:the conda environment is activated inside imagesGeniac CLI:options, init, install, test commands have been addedavailable on PyPI (https://pypi.org/project/geniac)Use the nextflow '-resume' options when building the configuration files en containersAdd params.yum to use 'dnf' instead of yum to install packages in the linux distrosNew custom target 'build_config_files'Minimal versions for nextflow (21.10.6) and singularity (3.8.5)environment.yml includes all dependencies required by geniac and geniac CLIBUGFIXCopy files in /usr/local/bin in the singularity image when the tool is built from source codeFix extra quotes in the beforeScript directive added in the conda.config and multiconda.config filesSome environment variables from the deffile were not correctly exported inside the imageDOCUMENTATIONHow to write singularity and docker recipes to activate conda environmentNew Miscellaneous sectionBinary or executable script: new use cases added as onlyLinux can not always be usedUpdates with new functionalities and modifications from version-2.0.0version-1.1.0
08/09/2021NEW FEATURESAdd retry errorStrategy in the nextflow.configNew cmake option ap_docker_registry to bootstrap on custom registry when building the containersbaseDir replaced by projectDirNew method to detect is the source directory is a git repositoryBUGFIXGeniac linter supports empty recipes folderDOCUMENTATIONUpdate the documentation and fix typosReference to the article addedCustom install section: add missing information where to save the custom recipesInstall from source code section: add missing link to modules/CMakeLists.txt templateversion-1.0.0
05/31/2021NEW FEATURESHarmonization of docker.nf / singularity.nf filesAdd missing indentation in singularity definition filesDOCUMENTATIONUpdate the documentation and fix typosversion-0.2.3
05/21/2021BUGFIXIn the dependencies section of the file environment.yml generated by geniac, pip has been addedDOCUMENTATIONUpdate the documentation and fix typosExample with the use of the cluster profile in useCases.bashversion-0.2.2
05/20/2021NEW FEATURESGeniac linter allows params.geniac.tools, params.geniac.containers.yum
and params.geniac.containers.git as optionalversion-0.2.1
05/19/2021NEW FEATURESOption ap_check_config_file_from_sourceGeniac linter support multiline comments in nf filesDOCUMENTATIONExamples to generate the containers recipesversion-0.2.0
03/30/2021NEW FEATURESGeniac command line interface (linter)version-0.1.2
03/26/2021DOCUMENTATIONUpdate documentation with geniac-demo-dsl2version-0.1.1
11/25/2020DOCUMENTATIONUpdate documentation with new labels for resource tuningversion-0.1.0
11/06/2020NEW FEATURESgeneration of the conda recipe environment.ymlcheckProfile* function added for path, multipath and singularity profilesreorganisation of the config files with geniac.config addedBUGFIXadd condition when empty modules folder is emptysymlink to singularity path can be createdversion-0.0.2NEW FEATURESutils folder has been renamed geniacversion-0.0.1NEW FEATURESset of utilities to build the containers and deploy the pipelineCeCILL FREE SOFTWARE LICENSE AGREEMENTVersion 2.1 dated 2013-06-21NoticeThis Agreement is a Free Software license agreement that is the result
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