From 86b70a409cfa533dca72f97c5000e603e15d60fd Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Fri, 6 Oct 2017 14:43:31 +0200
Subject: [PATCH 1/2] fixing curly bracket error in config file

---
 configuration/uppmax-localhost.config | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
index 1fc42a9e9c..d18f507b6e 100644
--- a/configuration/uppmax-localhost.config
+++ b/configuration/uppmax-localhost.config
@@ -60,14 +60,14 @@ process {
     memory = {params.totalMemory}
   }
   $IndelRealigner {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $MapReads {
     cpus = 16
     memory = {params.totalMemory}
   }
   $MarkDuplicates {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $MergeBams {
     cpus = 16
@@ -75,16 +75,16 @@ process {
   }
   $RealignerTargetCreator {
     cpus = 4
-    memory = params.singleCPUMem * 4 * task.attempt
+    memory = {params.singleCPUMem * 4 * task.attempt}
   }
   $RecalibrateBam {
     memory = {params.singleCPUMem * task.attempt}
   }
   $RunAlleleCount {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunAscat {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunBamQC {
     cpus = 16
@@ -93,18 +93,18 @@ process {
   $RunBcftoolsStats {
   }
   $RunConvertAlleleCounts {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunFastQC {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   $RunFreeBayes {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunHaplotypecaller {
     // Increase memory quadratically
-    memory = params.singleCPUMem * task.attempt * task.attempt
+    memory = {params.singleCPUMem * task.attempt * task.attempt}
   }
   $RunGenotypeGVCFs {
   }
@@ -116,16 +116,16 @@ process {
   }
   $RunMutect1 {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunMutect2 {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunSamtoolsStats {
   }
   $RunSnpeff {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
     memory = {params.totalMemory} // TODO Does SnpEff really require that much?
   }
   $RunStrelka {
@@ -133,7 +133,7 @@ process {
     memory = {params.totalMemory}
   }
   $RunVEP {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
     memory = {params.totalMemory} // TODO Does VEP really require that much?
   }
 }

From c230d589c5336a41ea5423219a2aef7d9a95254e Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Fri, 6 Oct 2017 14:55:27 +0200
Subject: [PATCH 2/2] update version

---
 buildContainers.nf | 2 +-
 buildReferences.nf | 2 +-
 main.nf            | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/buildContainers.nf b/buildContainers.nf
index 9f96cc54b6..2c19dac666 100644
--- a/buildContainers.nf
+++ b/buildContainers.nf
@@ -36,7 +36,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
diff --git a/buildReferences.nf b/buildReferences.nf
index 71a636b887..950f9059c0 100644
--- a/buildReferences.nf
+++ b/buildReferences.nf
@@ -39,7 +39,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented
diff --git a/main.nf b/main.nf
index 4b35746201..935a69c377 100644
--- a/main.nf
+++ b/main.nf
@@ -63,7 +63,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented