From 4dd0e85d5bb8cbb09fe4455ef1a8e12d57c0f49c Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Thu, 12 Mar 2020 16:31:57 +0100
Subject: [PATCH] add UMItools separator

---
 umi-tools.wdl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/umi-tools.wdl b/umi-tools.wdl
index 2d244c1..8defc8e 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -70,6 +70,7 @@ task Dedup {
     input {
         File inputBam
         File inputBamIndex
+        String umiSeparator = "_"
         String outputBamPath
         String? statsPrefix
         Boolean paired = true
@@ -89,6 +90,7 @@ task Dedup {
         --stdin ~{inputBam} \
         --stdout ~{outputBamPath} \
         ~{"--output-stats " + statsPrefix} \
+        --umi-separator=~{umiSeparator} \
         ~{true="--paired" false="" paired}
         samtools index ~{outputBamPath} ~{outputBamIndex}
     }
@@ -111,6 +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"}
         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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