diff --git a/library/tasks/HISAT2.wdl b/library/tasks/HISAT2.wdl
index 8498401b3..d4606a7d4 100644
--- a/library/tasks/HISAT2.wdl
+++ b/library/tasks/HISAT2.wdl
@@ -63,6 +63,8 @@ task HISAT2PairedEnd {
     # --seed to fix pseudo-random number and in order to produce deterministics results
     # --secondary reports secondary alignments for multimapping reads. -k 10
     # searches for up to 10 primary alignments for each read
+    mkfifo samtools_pipe
+    samtools view -1 -h -o "${output_basename}_unsorted.bam" samtools_pipe & pid=$!
     hisat2 -t \
       -x ${ref_name}/${ref_name} \
       -1 $FQ1 \
@@ -74,7 +76,8 @@ task HISAT2PairedEnd {
       --seed 12345 \
       -k 10 \
       --secondary \
-      -p ${cpu} -S >(samtools view -1 -h -o ${output_basename}_unsorted.bam)
+      -p ${cpu} -S samtools_pipe
+    wait $pid
     samtools sort -@ ${cpu} -O bam -o "${output_basename}.bam" "${output_basename}_unsorted.bam"
     samtools index "${output_basename}.bam"
   }
@@ -158,6 +161,8 @@ task HISAT2RSEM {
     # with no-splice-alignment no-softclip no-mixed options on, HISAT2 will only output concordant alignment without soft-cliping
     # --rdg 99999999,99999999 and --rfg 99999999,99999999 will set an infinite penalty to alignments with indels.
     # As a result, alignments with gaps or deletions are excluded.
+    mkfifo samtools_pipe
+    samtools view -1 -h -o "${output_basename}.bam" samtools_pipe & pid=$!
     hisat2 -t \
       -x ${ref_name}/${ref_name} \
       -1 $FQ1 \
@@ -178,7 +183,8 @@ task HISAT2RSEM {
       --rfg 99999999,99999999 \
       --no-spliced-alignment \
       --seed 12345 \
-      -p ${cpu} -S >(samtools view -1 -h -o ${output_basename}.bam)
+      -p ${cpu} -S samtools_pipe
+    wait $pid
   }
 
   runtime {
@@ -243,6 +249,8 @@ input {
     fi
 
     # The parameters for this task are copied from the HISAT2PairedEnd task.
+    mkfifo samtools_pipe
+    samtools view -1 -h -o "${output_basename}_unsorted.bam" samtools_pipe & pid=$!
     hisat2 -t \
       -x ~{ref_name}/~{ref_name} \
       -U $FQ \
@@ -253,9 +261,11 @@ input {
       --seed 12345 \
       -k 10 \
       --secondary \
-      -p ~{cpu} -S >(samtools view -1 -h -o ~{output_basename}_unsorted.bam)
+      -p ~{cpu} -S samtools_pipe
+    wait $pid
     samtools sort -@ ~{cpu} -O bam -o "~{output_basename}.bam" "~{output_basename}_unsorted.bam"
     samtools index "~{output_basename}.bam"
+
   }
 
   runtime {
@@ -375,6 +385,8 @@ task HISAT2RSEMSingleEnd {
     # with no-splice-alignment no-softclip no-mixed options on, HISAT2 will only output concordant alignment without soft-cliping
     # --rdg 99999999,99999999 and --rfg 99999999,99999999 will set an infinite penalty to alignments with indels.
     # As a result, alignments with gaps or deletions are excluded.
+    mkfifo samtools_pipe
+    samtools view -1 -h -o "${output_basename}.bam" samtools_pipe & pid=$!
     hisat2 -t \
       -x ${ref_name}/${ref_name} \
       -U $FQ \
@@ -394,7 +406,8 @@ task HISAT2RSEMSingleEnd {
       --rfg 99999999,99999999 \
       --no-spliced-alignment \
       --seed 12345 \
-      -p ${cpu} -S >(samtools view -1 -h -o ${output_basename}.bam)
+      -p ${cpu} -S samtools_pipe
+    wait $pid
   }
 
   runtime {