flowcraft/generator/engine.py
def _get_params_string(self):
        """Returns the nextflow params string from a dictionary object.

        The params dict should be a set of key:value pairs with the
        parameter name, and the default parameter value::

            self.params = {
                "genomeSize": 2.1,
                "minCoverage": 15
            }

        The values are then added to the string as they are. For instance,
        a ``2.1`` float will appear as ``param = 2.1`` and a
        ``"'teste'" string will appear as ``param = 'teste'`` (Note the
        string).

        Returns
        -------
        str
            Nextflow params configuration string
        """

        params_str = ""

        for p in self.processes:

            logger.debug("[{}] Adding parameters: {}\n".format(
                p.template, p.params)
            )

            # Add an header with the template name to structure the params
            # configuration
            if p.params and p.template != "init":

                p.set_param_id("_{}".format(p.pid))
                params_str += "\n\t/*"
                params_str += "\n\tComponent '{}_{}'\n".format(p.template,
                                                               p.pid)
                params_str += "\t{}\n".format("-" * (len(p.template) + len(p.pid) + 12))
                params_str += "\t*/\n"

            for param, val in p.params.items():

                if p.template == "init":
                    param_id = param
                else:
                    param_id = "{}_{}".format(param, p.pid)

                params_str += "\t{} = {}\n".format(param_id, val["default"])

        return params_str
def _get_params_string(self):
        """Returns the nextflow params string from a dictionary object.

        The params dict should be a set of key:value pairs with the
        parameter name, and the default parameter value::

            self.params = {
                "genomeSize": 2.1,
                "minCoverage": 15
            }

        The values are then added to the string as they are. For instance,
        a ``2.1`` float will appear as ``param = 2.1`` and a
        ``"'teste'" string will appear as ``param = 'teste'`` (Note the
        string).

        Returns
        -------
        str
            Nextflow params configuration string
        """

        params_str = ""

        for p in self.processes:

            logger.debug("[{}] Adding parameters: {}\n".format(
                p.template, p.params)
            )

            # Add an header with the template name to structure the params
            # configuration
            if p.params and p.template != "init":

                p.set_param_id("_{}".format(p.pid))
                params_str += "\n\t/*"
                params_str += "\n\tComponent '{}_{}'\n".format(p.template,
                                                               p.pid)
                params_str += "\t{}\n".format("-" * (len(p.template) + len(p.pid) + 12))
                params_str += "\t*/\n"

            for param, val in p.params.items():

                if p.template == "init":
                    param_id = param
                else:
                    param_id = "{}_{}".format(param, p.pid)

                params_str += "\t{} = {}\n".format(param_id, val["default"])

        return params_str
Returns the nextflow params string from a dictionary object.

        The params dict should be a set of key:value pairs with the
        parameter name, and the default parameter value::

            self.params = {
                "genomeSize": 2.1,
                "minCoverage": 15
            }

        The values are then added to the string as they are. For instance,
        a ``2.1`` float will appear as ``param = 2.1`` and a
        ``"'teste'" string will appear as ``param = 'teste'`` (Note the
        string).

        Returns
        -------
        str
            Nextflow params configuration string