main_wrapper

snakecdysis.cli_wrapper.main_wrapper(soft_path=None, url=None, docs=None, description_tool=None, apptainer_url_files=None, datatest_url_files=None, **kargs) → Group[source]

Use to wrapped snakemake workflow

Parameters:

  • soft_path (-) – The path of the wrapped workflow installation.

  • url (-) – URL of versioning repository (GitHub or GitLab).

  • docs (-) – URL of documentation.

  • description_tool (-) – The header printed on the terminal when running the program. Please include string values ‘VERSION’, ‘GIT_URL’, and ‘DOCS’, and the wrapper automatically replaces them with the correct values.

  • apptainer_url_files (-) – List of tuples with downloaded URL and install destination with INSTALL_PATH, like INSTALL_PATH/containers/Apptainer.CulebrONT_tools.sif.

  • datatest_url_files (-) – Tuple with 2 values, first the URL of datatest, second download name.

  • snakefile (-) – Path to the main Snakemake script file (default: snakefiles/snakefile).

  • snakemake_scripts (-) – Path to the main Snakemake script file (default: snakefiles/snakefile).

  • default_profile (-) – Path to create the cluster ‘default_profile’ directory (default: default_profile/).

  • git_configfile_path (-) – Path to the default configfile YAML (default: install_files/configfile.yaml).

  • git_tools_path (-) – Path to the default tools config YAML (default: install_files/tools_path.yaml).

  • git_profile_config (-) – Path to the default profile config file (default: install_files/config.yaml).

  • tools_version_path (-) – Path to the csv with soft and command to get version (default: snakemake_scripts/report_template/versions.csv).

  • slurm_mode_choice (-) – List of snakemake value for option –software-deployment-method (default: [‘env-modules’, ‘apptainer’, ‘conda’, “env-modules, conda”]).

  • local_mode_choice (-) – List of snakemake value for option –software-deployment-method (default: [‘apptainer’]).

Returns:

all sub-commands of workflow deployement and run

Return type:

click.Group (click.Group)

Exemple:
>>> from snakecdysis import main_wrapper
>>> from podiumASM import dico_tool
>>> main = main_wrapper(**dico_tool)
>>> main()
>>> main = main_wrapper(soft_path="path/to/install",
                        url="http://Snakecdysis.com",
                        docs=docs, description_tool=description_tool,
                        apptainer_url_files=[('http://nas-bgpi.myds.me/DOC/rattleSNP/Apptainer.rattleSNP_tools.sif',
                       'INSTALL_PATH/containers/Apptainer.rattleSNP_tools.sif'),
                      ('http://nas-bgpi.myds.me/DOC/rattleSNP/Apptainer.report.sif',
                       'INSTALL_PATH/containers/Apptainer.report.sif')
                        datatest_url_files=("http://nas-bgpi.myds.me/DOC/rattleSNP/data_test_rattleSNP.zip", "data_test_rattleSNP.zip")