From 5177db9da9ef24ada56c09d70933e339d374ae62 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 1 Nov 2010 14:55:42 -0700 Subject: [PATCH] Only complane about missing genomes if we _wanted_ to align the lane. If it was flagged for sequencing, don't complain. --- htsworkflow/pipelines/retrieve_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py index 3ba13fc..dd893e1 100644 --- a/htsworkflow/pipelines/retrieve_config.py +++ b/htsworkflow/pipelines/retrieve_config.py @@ -137,7 +137,7 @@ def format_gerald_config(options, flowcell_info, genome_map): species_path = genome_map.get(species, None) logging.debug("Looked for genome '%s' got location '%s'" % (species, species_path)) - if species_path is None: + if not is_sequencing and species_path is None: no_genome_msg = "Forcing lanes %s to sequencing as there is no genome for %s" logging.warning(no_genome_msg % (lane_numbers, species)) is_sequencing = True -- 2.30.2