From 0030b8b163ded5558513b4bc6b30a924577d7e52 Mon Sep 17 00:00:00 2001
From: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
Date: Wed, 25 Oct 2017 11:13:27 +0200
Subject: [PATCH 1/2] Adding exception handling to ASCAT when it is not able to
 find optimum

---
 bin/run_ascat.r | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/bin/run_ascat.r b/bin/run_ascat.r
index 31ea6f2264..e11c3f69c2 100755
--- a/bin/run_ascat.r
+++ b/bin/run_ascat.r
@@ -43,6 +43,12 @@ cnvs=ascat.output$segments[ascat.output$segments[,"nMajor"]!=1 | ascat.output$se
 write.table(cnvs, file=paste(tumorname,".cnvs.txt",sep=""), sep="\t", quote=F, row.names=F, col.names=T)
 
 #Write out purity and ploidy info
-summary <- matrix(c(ascat.output$aberrantcellfraction, ascat.output$ploidy), ncol=2, byrow=TRUE)
+summary <- tryCatch({
+		matrix(c(ascat.output$aberrantcellfraction, ascat.output$ploidy), ncol=2, byrow=TRUE)}, error = function(err) {
+			# error handler picks up where error was generated
+			print(paste("Could not find optimal solution:  ",err))
+			return(matrix(c(0,0),nrow=1,ncol=2,byrow = TRUE))
+		}
+)
 colnames(summary) <- c("AberrantCellFraction","Ploidy")
 write.table(summary, file=paste(tumorname,".purityploidy.txt",sep=""), sep="\t", quote=F, row.names=F, col.names=T)

From e3d71412c79d4a24f7fc56981491cb5bb47d2e5e Mon Sep 17 00:00:00 2001
From: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
Date: Wed, 25 Oct 2017 11:28:46 +0200
Subject: [PATCH 2/2] fixing config r-params-base typo

---
 configuration/singularity-path.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
index 4fb21e0ff2..8ce9cb3d93 100644
--- a/configuration/singularity-path.config
+++ b/configuration/singularity-path.config
@@ -33,10 +33,10 @@ process {
   $RealignerTargetCreator.container   = "${params.containerPath}/gatk-${params.tag}.img"
   $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
   $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
-  $RunAscat.container                 = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunAscat.container                 = "${params.containerPath}/r-base-${params.tag}.img"
   $RunBamQC.container                 = "${params.containerPath}/qualimap-${params.tag}.img"
   $RunBcftoolsStats.container         = "${params.containerPath}/caw-${params.tag}.img"
-  $RunConvertAlleleCounts.container   = "${params.containerPath}/r-params.base-${params.tag}.img"
+  $RunConvertAlleleCounts.container   = "${params.containerPath}/r-base-${params.tag}.img"
   $RunFastQC.container                = "${params.containerPath}/fastqc-${params.tag}.img"
   $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
   $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"