From e1806e2ea3946b6be28df6a39a234dc2a5a691c1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 18 May 2020 11:03:40 +0200
Subject: [PATCH] add summary file to hisat2 task
---
hisat2.wdl | 3 +++
1 file changed, 3 insertions(+)
diff --git a/hisat2.wdl b/hisat2.wdl
index bc6be2e..aafa333 100644
--- a/hisat2.wdl
+++ b/hisat2.wdl
@@ -31,6 +31,7 @@ task Hisat2 {
String readgroup
String platform = "illumina"
Boolean downstreamTranscriptomeAssembly = true
+ String summaryFilePath = basename(outputBam, ".bam") + ".summary.txt"
Int threads = 1
String memory = "48G"
@@ -55,6 +56,7 @@ task Hisat2 {
--rg 'LB:~{library}' \
--rg 'PL:~{platform}' \
~{true="--dta" false="" downstreamTranscriptomeAssembly} \
+ --summary-file ~{summaryFilePath} \
| samtools sort > ~{outputBam}
samtools index ~{outputBam} ~{bamIndexPath}
}
@@ -62,6 +64,7 @@ task Hisat2 {
output {
File bamFile = outputBam
File bamIndex = bamIndexPath
+ File summaryFile = summaryFilePath
}
runtime {
--
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