From da93300ad622d9332334ed1ccd32b2debe2b2ce6 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 31 Jan 2018 10:45:35 +0100
Subject: [PATCH] bugfixes'
---
bwa.wdl | 2 +-
spades.wdl | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index cafba38..04320ad 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -81,7 +81,7 @@ task mem {
${referenceFile} ${read1} ${read2}
}
output {
- File samFile = if defined(outputFile) then outputFile else stdout()
+ File samFile = if defined(outputFile) then select_first([outputFile]) else stdout()
}
runtime {
cpu: select_first([threads])
diff --git a/spades.wdl b/spades.wdl
index fd9b4ed..e4a150c 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -63,7 +63,7 @@ task spades {
${"--phred-offset " + phredOffset }
}
output {
- Array[File] correctedReads = glob_wildcard(outputDir + "/corrected/*.fastq*")
+ Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")
File scaffolds = outputDir + "/scaffolds.fasta"
File contigs = outputDir + "/contigs.fasta"
File assemblyGraphGfa = outputDir + "/assembly_graph.gfa"
--
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