From 5310007d64c92d491a0c2fd816f71aec52cccaf8 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Fri, 13 Mar 2020 13:09:40 +0100
Subject: [PATCH] umiSeparator made optional
---
umi-tools.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/umi-tools.wdl b/umi-tools.wdl
index 8defc8e..0a99d2b 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -70,7 +70,7 @@ task Dedup {
input {
File inputBam
File inputBamIndex
- String umiSeparator = "_"
+ String? umiSeparator
String outputBamPath
String? statsPrefix
Boolean paired = true
@@ -90,7 +90,7 @@ task Dedup {
--stdin ~{inputBam} \
--stdout ~{outputBamPath} \
~{"--output-stats " + statsPrefix} \
- --umi-separator=~{umiSeparator} \
+ ~{"--umi-separator=" + umiSeparator}
~{true="--paired" false="" paired}
samtools index ~{outputBamPath} ~{outputBamIndex}
}
@@ -113,7 +113,7 @@ task Dedup {
inputBamIndex: {description: "The index for the ipnut BAM file.", cateogry: "required"}
outputBamPath: {description: "The location to write the output BAM file to.", category: "required"}
statsPrefix: {description: "The prefix for the stats files.", category: "advanced"}
- umiSeparator: {description: "Seperator for UMI sequence, default with '_'", category: "advanced"}
+ umiSeparator: {description: "Seperator for UMI sequence", category: "advanced"}
paired: {description: "Whether or not the data is paired.", category: "common"}
memory: {description: "The amount of memory required for the task.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
--
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