From 8df42e20f13986734efb6fa085088bf85da8117d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 26 Jun 2020 11:07:26 +0200
Subject: [PATCH] do not require indexes on the markdup task
---
picard.wdl | 2 --
1 file changed, 2 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 3957539..69a1453 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -462,7 +462,6 @@ task GatherVcfs {
task MarkDuplicates {
input {
Array[File]+ inputBams
- Array[File] inputBamIndexes
String outputBamPath
String metricsPath
Int compressionLevel = 1
@@ -519,7 +518,6 @@ task MarkDuplicates {
parameter_meta {
# inputs
inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"}
- inputBamIndexes: {description: "Th eindexes for the input BAM files.", category: "required"}
outputBamPath: {description: "The location where the ouptut BAM file should be written.", category: "required"}
metricsPath: {description: "The location where the output metrics file should be written.", category: "required"}
read_name_regex: {description: "Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.", category: "advanced"}
--
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