From 3cbd0cb87d04085d214573a3316f760dad6f08cc Mon Sep 17 00:00:00 2001
From: Redmar <redmar@ubuntu.com>
Date: Mon, 29 Jun 2020 10:24:13 +0200
Subject: [PATCH] Add bam index to output

---
 pbmm2.wdl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pbmm2.wdl b/pbmm2.wdl
index 18d3cb9..84fbd2d 100644
--- a/pbmm2.wdl
+++ b/pbmm2.wdl
@@ -35,7 +35,6 @@ task Mapping {
     }
 
     command {
-        set -e
         pbmm2 align \
         --preset ~{presetOption} \
         ~{true="--sort" false="" sort} \
@@ -43,11 +42,11 @@ task Mapping {
         ~{referenceMMI} \
         ~{queryFile} \
         ~{sample}.align.bam
-
     }
 
     output {
         File outputAlignmentFile = sample + ".align.bam"
+        File outputIndexFile = sample + ".align.bam.bai"
     }
 
     runtime {
@@ -69,6 +68,7 @@ task Mapping {
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
 
         # output
-        outputAlignmentFile: {description: "Mapped bam files."}
+        outputAlignmentFile: {description: "Mapped bam file."}
+        outputIndexFile: {description: "Bam index file."}
     }
 }
-- 
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