From 5939f70504dc0497dfdcd189000b13fb2a937070 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 23 Oct 2018 15:08:41 +0200
Subject: [PATCH] Revert "add FixMateInformation"
This reverts commit ce2679ec1d6b262351714761450b1f9548765014.
---
picard.wdl | 41 -----------------------------------------
1 file changed, 41 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 5df7394..6a52ee4 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -199,47 +199,6 @@ task CollectTargetedPcrMetrics {
}
}
-task FixMateInformation {
- input {
- Array[File]+ inputBams
- Array[File]+ inputBamsIndex
- String outputBamPath
-
- String? preCommand
- String? picardJar
-
- Int memory = 4
- Float memoryMultiplier = 3.0
- }
-
- String toolCommand = if defined(picardJar)
- then "java -Xmx" + memory + "G -jar " + picardJar
- else "picard -Xmx" + memory + "G"
-
- command {
- set -e -o pipefail
- ~{preCommand}
- ~{toolCommand} \
- FixMateInformation \
- INPUT=~{sep=' INPUT=' inputBams} \
- OUTPUT=~{outputBamPath} \
- CREATE_INDEX=true \
- CREATE_MD5_FILE=true
- }
-
- output {
- IndexedBamFile outputBam = object {
- file: outputBamPath,
- index: sub(outputBamPath, ".bam$", ".bai"),
- md5: outputBamPath + ".md5"
- }
- }
-
- runtime {
- memory: ceil(memory * memoryMultiplier)
- }
-}
-
# Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs
task GatherBamFiles {
input {
--
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