From 8aaf9153965f7e4e5a4b3ebf08b467c7faca7c2e Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 17 May 2018 13:33:15 +0200
Subject: [PATCH] call caching fixes
---
biopet.wdl | 6 ++++--
samtools.wdl | 2 +-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 93dab22..dcd7014 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -60,6 +60,7 @@ task SampleConfig {
String? preCommand
String tool_jar
Array[File]+ inputFiles
+ String keyFilePath
String? sample
String? library
String? readgroup
@@ -80,11 +81,12 @@ task SampleConfig {
${"--library " + library} \
${"--readgroup " + readgroup} \
${"--jsonOutput " + jsonOutputPath} \
- ${"--tsvOutput " + tsvOutputPath}
+ ${"--tsvOutput " + tsvOutputPath} \
+ > ${keyFilePath}
}
output {
- File keysFile = stdout()
+ File keysFile = keyFilePath
File? jsonOutput = jsonOutputPath
File? tsvOutput = tsvOutputPath
}
diff --git a/samtools.wdl b/samtools.wdl
index a1192ac..80dd792 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -1,6 +1,6 @@
task Index {
String? preCommand
- String bamFilePath
+ File bamFilePath
command {
set -e -o pipefail
--
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