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Adding exception handling to ASCAT when it is not able to find optimum #489

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maxulysse merged 2 commits into from
Oct 27, 2017
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Adding exception handling to ASCAT when it is not able to find optimum #489

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0030b8b
Adding exception handling to ASCAT when it is not able to find optimum
Oct 25, 2017
e3d7141
fixing config r-params-base typo
Oct 25, 2017
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8 changes: 7 additions & 1 deletion bin/run_ascat.r
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
4 changes: 2 additions & 2 deletions configuration/singularity-path.config
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Expand Up @@ -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"
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