From a0933e34c55d4bed26510e0fd09fe013441898c1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 18 Jan 2022 14:38:42 +0100
Subject: [PATCH] Add option to assume sort order
---
picard.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/picard.wdl b/picard.wdl
index bf32c8a..144c778 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -1038,6 +1038,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
String outputPath
String outputPathMetrics = outputPath + ".metrics"
String outputPathUmiMetrics = outputPath + ".umi-metrics"
+ String? assumeSortOrder
String tempdir = "temp"
Boolean removeDuplicates = true
String umiTagName = "RX"
@@ -1065,7 +1066,8 @@ task UmiAwareMarkDuplicatesWithMateCigar {
CREATE_INDEX=true \
COMPRESSION_LEVEL=~{compressionLevel} \
USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
- USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}
+ USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater} \
+ ~{"ASSUME_SORT_ORDER=" + assumeSortOrder}
}
output {
@@ -1089,6 +1091,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
outputPathUmiMetrics: {description: "The location the output UMI metrics file should be written to.", category: "required"}
removeDuplicates: {description: "Whether the duplicate reads should be removed instead of marked.", category: "common"}
umiTagName: {description: "Which tag in the BAM file holds the UMI.", category: "common"}
+ assumeSortOrder: {description: "Assume a certain sort order even though the header might say otherwise.", category: "common"}
tempdir: {description: "Temporary directory.", category: "advanced"}
compressionLevel: {description: "The compression level at which the BAM files are written.", category: "advanced"}
useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
--
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