From 8ccabed5e8c56d2f742d5aba829104fe8db00d2d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 4 Jan 2022 14:10:45 +0100
Subject: [PATCH] Allow multiple bam inputs
---
picard.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index d8ce5eb..d2a6ca3 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -1007,7 +1007,7 @@ task RenameSample {
task UmiAwareMarkDuplicatesWithMateCigar {
input {
- File inputBam
+ Array[File] inputBams
String outputPath
String outputPathMetrics = outputPath + ".metrics"
String outputPathUmiMetrics = outputPath + ".umi-metrics"
@@ -1023,7 +1023,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
set -e
mkdir -p "$(dirname ~{outputPath})" ~{tempdir}
picard UmiAwareMarkDuplicatesWithMateCigar \
- I=~{inputBam} \
+ INPUT=~{sep=' INPUT=' inputBams} \
O=~{outputPath} \
M=~{outputPathMetrics} \
UMI_METRICS_FILE=~{outputPathUmiMetrics} \
@@ -1047,7 +1047,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
parameter_meta {
# inputs
- inputBam: {description: "The unsorted input BAM file.", category: "required"}
+ inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
outputPathMetrics: {description: "The location the output metrics file should be written to.", category: "required"}
outputPathUmiMetrics: {description: "The location the output UMI metrics file should be written to.", category: "required"}
--
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