diff --git a/docs/workflow_users/workflow_deployment.rst b/docs/workflow_users/workflow_deployment.rst index f346bde..18b8f27 100644 --- a/docs/workflow_users/workflow_deployment.rst +++ b/docs/workflow_users/workflow_deployment.rst @@ -35,8 +35,8 @@ For the example above, it will have the following content use rule * from dna_seq_varlociraptor utilizing `Snakemake's module system `__. -In addition, it will copy over the contents of the ``config`` directory of the given repository into ``/tmp/dest/workflow/Snakefile``. -These should be seen as a template, can be modified according to your needs. +In addition, it will copy over the ``config/`` and ``profiles/`` directories of the given repository (and their contents) into respective directories under ``/tmp/dest/``. +These should be seen as templates, and can be modified according to your needs. Further, the workflow definition Snakefile can be arbitrarily extended and modified, thereby making any changes to the used workflow transparent (also see the `snakemake module documentation `_). It is highly advisable to put the deployed workflow into a new (perhaps private) git repository (e.g., see `here `_ for instructions how to do that with Github).