From b05b94e3de56169831178171ee45dedeb21bfc7f Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Thu, 6 Jun 2019 16:05:24 -0400
Subject: [PATCH] in picard demux set max_mismatches=0

for more stringent demux, in picard demux set max_mismatches=0, from max_mismatches=1
---
 pipes/WDL/workflows/tasks/tasks_demux.wdl | 2 +-
 tools/picard.py                           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipes/WDL/workflows/tasks/tasks_demux.wdl b/pipes/WDL/workflows/tasks/tasks_demux.wdl
index 18132f5c3..2a01738be 100644
--- a/pipes/WDL/workflows/tasks/tasks_demux.wdl
+++ b/pipes/WDL/workflows/tasks/tasks_demux.wdl
@@ -37,7 +37,7 @@ task illumina_demux {
 
   String? flowcell
   Int?    minimumBaseQuality = 10
-  Int?    maxMismatches = 1
+  Int?    maxMismatches = 0
   Int?    minMismatchDelta
   Int?    maxNoCalls
   String? readStructure
diff --git a/tools/picard.py b/tools/picard.py
index 2ef2891a5..22b6dc75b 100644
--- a/tools/picard.py
+++ b/tools/picard.py
@@ -458,7 +458,7 @@ def execute(
 class ExtractIlluminaBarcodesTool(PicardTools):
     subtoolName = 'ExtractIlluminaBarcodes'
     jvmMemDefault = '8g'
-    defaults = {'read_structure': '101T8B8B101T', 'max_mismatches': 1, 'minimum_base_quality': 10, 'num_processors': 0}
+    defaults = {'read_structure': '101T8B8B101T', 'max_mismatches': 0, 'minimum_base_quality': 10, 'num_processors': 0}
     option_list = (
         'read_structure', 'max_mismatches', 'minimum_base_quality', 'min_mismatch_delta', 'max_no_calls',
         'minimum_quality', 'compress_outputs', 'num_processors'