From abdec8e2f95b13c0301072d2538624360a9d9f94 Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Mon, 9 Sep 2019 15:17:52 +0200
Subject: [PATCH] Removed "pipefail" from command sections TALON and
 TranscriptClean because no pipes are used. (Based on minimap2.wdl pull
 request)

---
 CHANGELOG.md        |  1 +
 talon.wdl           | 14 +++++++-------
 transcriptclean.wdl | 10 +++++-----
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f6ca40b..ce22473 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 b9eaebc..507e0b9 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 44cc35d..7afd241 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} \
-- 
GitLab