diff --git a/CHANGELOG.md b/CHANGELOG.md
index f6ca40b3a26795234abe82a58aef2780b950dba7..ce2247333cc077426083ac9cb04f707603be2bcb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ Removed "pipefail" from command sections TALON and TranscriptClean
 + Add WDL task for Minimap2
 + Add WDL task for TALON
 + Add WDL task for TranscriptClean
diff --git a/talon.wdl b/talon.wdl
index b9eaebcd9964262d677f773e1150cd016f9796b4..507e0b9a3440a85a6109d81d2fb94d0c648e6343 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -36,7 +36,7 @@ task CreateAbundanceFileFromDatabase {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         create_abundance_file_from_database \
         ~{"--db=" + databaseFile} \
@@ -85,7 +85,7 @@ task CreateGtfAbundanceFromDatabase {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         create_GTF_abundance_from_database \
         ~{"--db=" + databaseFile} \
@@ -137,7 +137,7 @@ task CreateGtfFromDatabase {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         create_GTF_from_database \
         ~{"--db=" + databaseFile} \
@@ -189,7 +189,7 @@ task InitializeTalonDatabase {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         initialize_talon_database \
         ~{"--f=" + GTFfile} \
@@ -238,7 +238,7 @@ task MapAntisenseGenesToSense {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         map_antisense_genes_to_sense \
         ~{"--db=" + databaseFile} \
@@ -278,7 +278,7 @@ task SummarizeDatasets {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         summarize_datasets \
         ~{"--db " + databaseFile} \
@@ -323,7 +323,7 @@ task Talon {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         mv ${configFile} ./${configFileName}
         mv ${SAMfile} ./${SAMfileName}
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index 44cc35dcc5d57e08154dcddd18f89a44ac44744d..7afd24197084d5ac318b07a15bc2692b38ece5f5 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -35,7 +35,7 @@ task CleanSpliceJunctions {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         clean_splice_jns \
         ~{"--f=" + SAMfile} \
@@ -77,7 +77,7 @@ task GetCorrectedSJsFromLog {
     }
 
     command {
-        set -e pipefail
+        set -e 
         mkdir -p $(dirname ~{outputPrefix})
         get_corrected_SJs_from_log \
         ~{TElogFile} \
@@ -115,7 +115,7 @@ task GetSJsFromGtf {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         get_SJs_from_gtf \
         ~{"--f=" + GTFfile} \
@@ -155,7 +155,7 @@ task GetTranscriptCleanStats {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         get_TranscriptClean_stats \
         ~{transcriptCleanSAMfile} \
@@ -202,7 +202,7 @@ task TranscriptClean {
     }
 
     command {
-        set -e pipefail
+        set -e
         mkdir -p $(dirname ~{outputPrefix})
         TranscriptClean \
         ~{"-s " + SAMfile} \