add limitBAMsortRAM

gatk.wdl

@@ -271,7 +271,7 @@ task SplitNCigarReads {
         SplitNCigarReads \
         -I ${input_bam} \
         -R ${ref_fasta} \
-        -O ${output_bam} # might have to be -o depending on GATK version \
+        -O ${output_bam} \
         -L ${sep=' -L ' intervals}
     }
 

star.wdl

@@ -12,6 +12,7 @@ task Star {
     String? outStd
     String? twopassMode
     Array[String]? outSAMattrRGline
+    Int? limitBAMsortRAM
 
     Int? memory
 
@@ -34,6 +35,7 @@ task Star {
         ${"--runThreadN " + runThreadN} \
         ${"--outStd " + outStd} \
         ${"--twopassMode " + twopassMode} \
+        ${"--limitBAMsortRAM " + limitBAMsortRAM} \
         ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline}
     }