From a73fd8a65f7ccb6e20f712f2129432057a8e0349 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 Mar 2022 12:15:51 +0100
Subject: [PATCH] Add parameter_meta for useSoftclippingforSupplementary
---
bwa.wdl | 1 +
1 file changed, 1 insertion(+)
diff --git a/bwa.wdl b/bwa.wdl
index 1cb170b..373de62 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -94,6 +94,7 @@ task Mem {
outputPrefix: {description: "The prefix of the output files, including any parent directories.", category: "required"}
sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
usePostalt: {description: "Whether to use the postalt script from bwa kit."}
+ useSoftclippingForSupplementary: {description: "Use soft-clipping for supplementary alignments instead of hard-clipping", category: "common"}
sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
readgroup: {description: "A readgroup identifier.", category: "common"}
--
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