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"])
def _set_secondary_channels ( self ) : 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.
Sets the secondary channels for the pipeline