main_wrapper

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

Use to wrapped snakemake workflow

Parameters:

  • soft_path (str) – The path of wrapped workflow installation

  • url (str) – Url of versioning repository (GitHub or GitLab)

  • docs (str) – Url of documentation

  • description_tool (str) – The header print on terminal when run programme. Please add string values ‘VERSION’, ‘GIT_URL’ and ‘DOCS’ and wrapper automatically replace by th good values

  • singularity_url_files (list(tuple()) – List of tuple with singularity downloaded url and install destination path, with INSTALL_PATH. like INSTALL_PATH/containers/Singularity.CulebrONT_tools.sif

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

  • snakefile (str) – Path to main snakemake script file (default: PKGNAME/snakefiles/snakefile)

  • snakemake_scripts (str) – Path to main snakemake script file (default: PKGNAME/snakefiles/snakefile)

  • default_profile (str) – Path to create ths cluster ‘default_profile’ directory (default: PKGNAME/default_profile/)

  • git_config_path (str) – Path to default config file yaml (default: PKGNAME/install_files/config.yaml)

  • git_tools_path (str) – Path to default tools config yaml(default: PKGNAME/install_files/tools_path.yaml)

  • git_cluster_config (str) – Path to slurm cluster config file (default: PKGNAME/install_files/cluster_config_SLURM.yaml)

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,
                        singularity_url_files=[('http://nas-bgpi.myds.me/DOC/rattleSNP/Singularity.rattleSNP_tools.sif',
                       'INSTALL_PATH/containers/Singularity.rattleSNP_tools.sif'),
                      ('http://nas-bgpi.myds.me/DOC/rattleSNP/Singularity.report.sif',
                       'INSTALL_PATH/containers/Singularity.report.sif')
                        datatest_url_files=("http://nas-bgpi.myds.me/DOC/rattleSNP/data_test_rattleSNP.zip", "data_test_rattleSNP.zip")