flowcraft/generator/engine.py
def _set_secondary_channels(self):
        """Sets the secondary channels for the pipeline

        This will iterate over the
        :py:attr:`NextflowGenerator.secondary_channels` dictionary that is
        populated when executing
        :func:`~NextflowGenerator._update_secondary_channels` method.
        """

        logger.debug("==========================")
        logger.debug("Setting secondary channels")
        logger.debug("==========================")

        logger.debug("Setting secondary channels: {}".format(
            self.secondary_channels))

        for source, lanes in self.secondary_channels.items():

            for vals in lanes.values():

                if not vals["end"]:
                    logger.debug("[{}] No secondary links to setup".format(
                        vals["p"].template))
                    continue

                logger.debug("[{}] Setting secondary links for "
                             "source {}: {}".format(vals["p"].template,
                                                    source,
                                                    vals["end"]))

                vals["p"].set_secondary_channel(source, vals["end"])
def _set_secondary_channels(self):
        """Sets the secondary channels for the pipeline

        This will iterate over the
        :py:attr:`NextflowGenerator.secondary_channels` dictionary that is
        populated when executing
        :func:`~NextflowGenerator._update_secondary_channels` method.
        """

        logger.debug("==========================")
        logger.debug("Setting secondary channels")
        logger.debug("==========================")

        logger.debug("Setting secondary channels: {}".format(
            self.secondary_channels))

        for source, lanes in self.secondary_channels.items():

            for vals in lanes.values():

                if not vals["end"]:
                    logger.debug("[{}] No secondary links to setup".format(
                        vals["p"].template))
                    continue

                logger.debug("[{}] Setting secondary links for "
                             "source {}: {}".format(vals["p"].template,
                                                    source,
                                                    vals["end"]))

                vals["p"].set_secondary_channel(source, vals["end"])
Sets the secondary channels for the pipeline

        This will iterate over the
        :py:attr:`NextflowGenerator.secondary_channels` dictionary that is
        populated when executing
        :func:`~NextflowGenerator._update_secondary_channels` method.