Merge pull request #421 from broadinstitute/ct-expose-ref-guided-cons…

…ensus-novo-params expose in the config the parameters passed to Novoalign for refining the reference-guided consensus
broadinstitute · Jul 28, 2016 · cd4a8ac · cd4a8ac
2 parents a7f6a6f + 086768b
commit cd4a8ac
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/pipes/config.yaml b/pipes/config.yaml
@@ -135,6 +135,9 @@ refine_assembly_2_novoalign_params: "-r Random -l 40 -g 40 -x 20 -t 100"
 # parameters passed to Novoalign for mapping reads back to the consensus
 map_reads_to_self_novoalign_params: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
 
+# parameters passed to Novoalign for refining the reference-guided consensus
+ref_guided_consensus_novoalign_params: "-r Random -l 30 -g 40 -x 20 -t 502"
+
 # Alignment parameters for nucmer (MUMmer) during the scaffolding step.
 # Shown below are defaults.
 #assembly_nucmer_max_gap: 200

diff --git a/pipes/rules/interhost.rules b/pipes/rules/interhost.rules
@@ -44,7 +44,7 @@ rule ref_guided_consensus:
  params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
  UGER=config.get('UGER_queues', {}).get('short', '-q short'),
  logid="{sample}",
- novoalign_options="-r Random -l 30 -g 40 -x 20 -t 502",
+ novoalign_options=config.get("ref_guided_consensus_novoalign_params", "-r Random -l 30 -g 40 -x 20 -t 502"),
  min_coverage="3",
  numThreads=str(config.get("number_of_threads", 1))
  run: