flowcraft/generator/engine.py
def _set_configurations(self):
        """This method will iterate over all process in the pipeline and
        populate the nextflow configuration files with the directives
        of each process in the pipeline.
        """

        logger.debug("======================")
        logger.debug("Setting configurations")
        logger.debug("======================")

        resources = ""
        containers = ""
        params = ""
        manifest = ""

        if self.merge_params:
            params += self._get_merged_params_string()
            help_list = self._get_merged_params_help()
        else:
            params += self._get_params_string()
            help_list = self._get_params_help()

        for p in self.processes:

            # Skip processes with the directives attribute populated
            if not p.directives:
                continue

            logger.debug("[{}] Adding directives: {}".format(
                p.template, p.directives))
            resources += self._get_resources_string(p.directives, p.pid)
            containers += self._get_container_string(p.directives, p.pid)

        manifest = self._get_manifest_string()

        self.resources = self._render_config("resources.config", {
            "process_info": resources
        })
        self.containers = self._render_config("containers.config", {
            "container_info": containers
        })
        self.params = self._render_config("params.config", {
            "params_info": params
        })
        self.manifest = self._render_config("manifest.config", {
            "manifest_info": manifest
        })
        self.help = self._render_config("Helper.groovy", {
            "nf_file": basename(self.nf_file),
            "help_list": help_list,
            "version": __version__,
            "pipeline_name": " ".join([x.upper() for x in self.pipeline_name])
        })
        self.user_config = self._render_config("user.config", {})
def _set_configurations(self):
        """This method will iterate over all process in the pipeline and
        populate the nextflow configuration files with the directives
        of each process in the pipeline.
        """

        logger.debug("======================")
        logger.debug("Setting configurations")
        logger.debug("======================")

        resources = ""
        containers = ""
        params = ""
        manifest = ""

        if self.merge_params:
            params += self._get_merged_params_string()
            help_list = self._get_merged_params_help()
        else:
            params += self._get_params_string()
            help_list = self._get_params_help()

        for p in self.processes:

            # Skip processes with the directives attribute populated
            if not p.directives:
                continue

            logger.debug("[{}] Adding directives: {}".format(
                p.template, p.directives))
            resources += self._get_resources_string(p.directives, p.pid)
            containers += self._get_container_string(p.directives, p.pid)

        manifest = self._get_manifest_string()

        self.resources = self._render_config("resources.config", {
            "process_info": resources
        })
        self.containers = self._render_config("containers.config", {
            "container_info": containers
        })
        self.params = self._render_config("params.config", {
            "params_info": params
        })
        self.manifest = self._render_config("manifest.config", {
            "manifest_info": manifest
        })
        self.help = self._render_config("Helper.groovy", {
            "nf_file": basename(self.nf_file),
            "help_list": help_list,
            "version": __version__,
            "pipeline_name": " ".join([x.upper() for x in self.pipeline_name])
        })
        self.user_config = self._render_config("user.config", {})
This method will iterate over all process in the pipeline and
        populate the nextflow configuration files with the directives
        of each process in the pipeline.