From: Diane Trout <diane@caltech.edu>
Date: Mon, 1 Nov 2010 21:55:42 +0000 (-0700)
Subject: Only complane about missing genomes if we _wanted_ to align the lane.
X-Git-Tag: 0.5.0~17
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=5177db9da9ef24ada56c09d70933e339d374ae62

Only complane about missing genomes if we _wanted_ to align the lane.
If it was flagged for sequencing, don't complain.
---

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