From 086768b5d0835158ea6a77c443d724f4aa519d53 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 28 Jul 2016 16:14:12 -0400 Subject: [PATCH] expose in the config the parameters passed to Novoalign for refining the reference-guided consensus --- pipes/config.yaml | 3 +++ pipes/rules/interhost.rules | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/pipes/config.yaml b/pipes/config.yaml index 943b5f721..e0bc5c34e 100644 --- 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 index e2b436446..9b28193f6 100644 --- 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: