From 6de757570c8bb135aa2315436788d64eac2e7e4b Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Wed, 12 Sep 2018 13:39:56 +0200
Subject: [PATCH] Fixed names
---
gatk.wdl | 7 +++----
picard.wdl | 1 +
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index bd920bf..970f6a5 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -40,12 +40,11 @@ task ApplyBQSR {
}
output {
- IndexedBamFile recalibrated_bam = {
+ IndexedBamFile recalibratedBam = {
"file": outputBamPath,
- "index": sub(outputBamPath, "\.bam$", ".bai")
+ "index": sub(outputBamPath, "\.bam$", ".bai"),
+ "md5": outputBamPath + ".md5"
}
-
- File recalibrated_bam_checksum = outputBamPath + ".md5"
}
runtime {
diff --git a/picard.wdl b/picard.wdl
index 6fcf6b6..6a52ee4 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -204,6 +204,7 @@ task GatherBamFiles {
input {
String? preCommand
Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
String outputBamPath
String? picardJar
--
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