From a0de5e64323c47a390851719af2781f4096ddb9f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 Jun 2018 14:30:32 +0200
Subject: [PATCH 1/2] add validatefastq

---
 biopet.wdl | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/biopet.wdl b/biopet.wdl
index 286b2e0..b6fa893 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -305,3 +305,27 @@ task Seqstat {
     }
 }
 
+task ValidateFastq {
+    String? preCommand
+    File? toolJar
+    File fastq1
+    File? fastq2
+
+    Float? memory
+    Float? memoryMultiplier
+    Int mem = ceil(select_first([memory, 4.0]))
+
+    String toolCommand = if defined(toolJar)
+    then "java -Xmx" + mem + "G -jar " + toolJar
+    else "biopet-validatefastq -Xmx" + mem + "G"
+
+    command {
+        set -e -o pipefail
+        ${preCommand}
+        biopet-validatefastq \
+        --fastq1 ${fastq1} \
+        ${"--fastq2 " + fastq2}
+    }
+
+}
+
-- 
GitLab


From 4382c7b73bd1403cbf1e46af7da4e3c41a01200b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 Jun 2018 16:30:19 +0200
Subject: [PATCH 2/2] add stderr

---
 biopet.wdl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/biopet.wdl b/biopet.wdl
index b6fa893..9103069 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -326,6 +326,8 @@ task ValidateFastq {
         --fastq1 ${fastq1} \
         ${"--fastq2 " + fastq2}
     }
-
+    output {
+        File stderr = stderr()
+    }
 }
 
-- 
GitLab