main_wrapper

snakecdysis.cli_wrapper.main_wrapper(dico_tool=None, 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

  • dico_tool (dict) – The dict structure provided of wrapped workflow

  • or –

  • 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 downloaded url and install destination 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.

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_ur_files=singularity_url_files, datatest_url_files=datatest_url_files)