Merge pull request #36 from CCRGeneticsBranch/develop

Develop
CCRGeneticsBranch · Oct 16, 2024 · 9d2e302 · 9d2e302
2 parents 0f302da + d77bfbc
commit 9d2e302
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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
@@ -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}":