diff --git a/config/biowulf_small_test_params.config b/config/biowulf_small_test_params.config index 5ee5d1d..030064c 100755 --- a/config/biowulf_small_test_params.config +++ b/config/biowulf_small_test_params.config @@ -1,5 +1,5 @@ params { - Pipeline_version = "5.1" + Pipeline_version = "5.1.1" genome_version = "19" genome_version_tcellextrect = "hg19" genome_version_fusion_annotation = "v37lift37" diff --git a/main.nf b/main.nf index f512067..9889699 100755 --- a/main.nf +++ b/main.nf @@ -101,7 +101,7 @@ workflow.onComplete { //sendMail(to: "${workflow.userName}@mail.nih.gov" , subject: 'khanlab ngs-pipeline execution successful', body: fullMessage, mimeType: 'text/html') - sendMail(to: "${workflow.userName}@mail.nih.gov" , cc: 'khanjav@mail.nih.gov, weij@mail.nih.gov, wenxi@mail.nih.gov, gangalapudiv2@mail.nih.gov,' , subject: 'khanlab ngs-pipeline execution successful', body: fullMessage, mimeType: 'text/html') + sendMail(to: "${workflow.userName}@mail.nih.gov" , cc: 'wenxi@mail.nih.gov, gangalapudiv2@mail.nih.gov,' , subject: 'khanlab ngs-pipeline execution successful', body: fullMessage, mimeType: 'text/html') } } else { diff --git a/modules/RNAseq_GATK/GATK.nf b/modules/RNAseq_GATK/GATK.nf index a63c513..d79ff86 100755 --- a/modules/RNAseq_GATK/GATK.nf +++ b/modules/RNAseq_GATK/GATK.nf @@ -48,7 +48,7 @@ process GATK_RTC_IR { java -jar -Xmx40g \$GATK_JAR -T RealignerTargetCreator -nt 10 -R $genome -known $phase1_1000g -known $Mills_and_1000g -I $bam -o ${meta.lib}.realignment.intervals - java -jar -Xmx40g \$GATK_JAR -T IndelRealigner -R $genome -known $phase1_1000g -known $Mills_and_1000g -I $bam --targetIntervals ${meta.lib}.realignment.intervals -o ${meta.lib}.Ir.bam + java -jar -Xmx40g \$GATK_JAR -T IndelRealigner -R $genome -known $phase1_1000g -known $Mills_and_1000g -I $bam --targetIntervals ${meta.lib}.realignment.intervals -o ${meta.lib}.Ir.bam --maxReadsInMemory 1500000 cat <<-END_VERSIONS > versions.yml "${task.process}":