From 9c02efccc8fbc4db6f3656f263a776508944e380 Mon Sep 17 00:00:00 2001 From: igor Date: Mon, 7 Aug 2017 14:53:52 -0400 Subject: [PATCH] update gatk --- run | 2 +- segments/bam-ra-rc-gatk.sh | 2 +- segments/bam-splitncigar-gatk.sh | 2 +- segments/qc-coverage-gatk.sh | 2 +- segments/qc-target-reads-gatk.sh | 2 +- segments/snvs-gatk-hc.sh | 2 +- segments/snvs-mutect2.sh | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/run b/run index 8c80f06..cc021fb 100755 --- a/run +++ b/run @@ -128,7 +128,7 @@ sub run_samples { chomp(@unique_samples); # check that sample names do not contain problematic characters - my @invalid_samples = grep(/[^\w\-\.]/, @unique_samples); + my @invalid_samples = grep(/[^\w\-\.\:]/, @unique_samples); if (@invalid_samples) { my $invalid_samples_str = join(', ', @invalid_samples); die "\n\n ERROR: SAMPLES $invalid_samples_str CONTAIN PROBLEMATIC CHARACTERS \n\n"; diff --git a/segments/bam-ra-rc-gatk.sh b/segments/bam-ra-rc-gatk.sh index a262a88..a355897 100755 --- a/segments/bam-ra-rc-gatk.sh +++ b/segments/bam-ra-rc-gatk.sh @@ -129,7 +129,7 @@ module load r/3.3.0 module unload zlib # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}" if [ ! -s "$gatk_jar" ] ; then diff --git a/segments/bam-splitncigar-gatk.sh b/segments/bam-splitncigar-gatk.sh index ae816b2..a7c086f 100755 --- a/segments/bam-splitncigar-gatk.sh +++ b/segments/bam-splitncigar-gatk.sh @@ -99,7 +99,7 @@ module load java/1.8 module load r/3.3.0 # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}" if [ ! -s "$gatk_jar" ] ; then diff --git a/segments/qc-coverage-gatk.sh b/segments/qc-coverage-gatk.sh index 4c23cb6..851e21d 100755 --- a/segments/qc-coverage-gatk.sh +++ b/segments/qc-coverage-gatk.sh @@ -100,7 +100,7 @@ module unload java module load java/1.8 # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}" if [ ! -s "$gatk_jar" ] ; then diff --git a/segments/qc-target-reads-gatk.sh b/segments/qc-target-reads-gatk.sh index aa5fe39..21a1993 100755 --- a/segments/qc-target-reads-gatk.sh +++ b/segments/qc-target-reads-gatk.sh @@ -104,7 +104,7 @@ module unload java module load java/1.8 # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar $gatk_jar" gatk_omit_arg="--omitIntervalStatistics --omitLocusTable --omitDepthOutputAtEachBase" diff --git a/segments/snvs-gatk-hc.sh b/segments/snvs-gatk-hc.sh index 402b914..d3944d7 100755 --- a/segments/snvs-gatk-hc.sh +++ b/segments/snvs-gatk-hc.sh @@ -96,7 +96,7 @@ module unload java module load java/1.8 # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}" # error log (DEBUG, INFO (default), WARN, ERROR, FATAL, OFF) diff --git a/segments/snvs-mutect2.sh b/segments/snvs-mutect2.sh index 58529e4..e98a181 100755 --- a/segments/snvs-mutect2.sh +++ b/segments/snvs-mutect2.sh @@ -111,7 +111,7 @@ module unload java module load java/1.8 # command -gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar" +gatk_jar="/ifs/home/id460/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-0/GenomeAnalysisTK.jar" gatk_cmd="java -Xms16G -Xmx16G -jar ${gatk_jar}" if [ ! -s "$gatk_jar" ] ; then