From 7e8c833eadb0259da33e6d641393f77dbe3f2578 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Wed, 22 Jul 2020 11:54:00 +0200
Subject: [PATCH] Fix tests.
---
transcriptclean.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index daf7970..6e0de8a 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -109,7 +109,7 @@ task GetTranscriptCleanStats {
task TranscriptClean {
input {
- File samFile
+ File inputSam
File referenceGenome
Int maxLenIndel = 5
Int maxSJOffset = 5
@@ -136,7 +136,7 @@ task TranscriptClean {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
TranscriptClean \
- -s ~{samFile} \
+ -s ~{inputSam} \
-g ~{referenceGenome} \
-t ~{cores} \
--maxLenIndel=~{maxLenIndel} \
@@ -170,7 +170,7 @@ task TranscriptClean {
parameter_meta {
# inputs
- samFile: {description: "Input sam file containing transcripts to correct.", category: "required"}
+ inputSam: {description: "Input sam file containing transcripts to correct.", category: "required"}
referenceGenome: {description: "Reference genome fasta file.", category: "required"}
maxLenIndel: {description: "Maximum size indel to correct.", category: "advanced"}
maxSJOffset: {description: "Maximum distance from annotated splice junction to correct.", category: "advanced"}
--
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