Merge pull request #140 from biowdl/BIOWDL-269

Removed "pipefail" from command sections TALON and TranscriptClean

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

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}

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} \