From 5e572ffcf5057fb2ac90bbde90f21e27936dc793 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Wed, 22 Jul 2020 11:57:23 +0200
Subject: [PATCH] Fix some input naming.
---
transcriptclean.wdl | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/transcriptclean.wdl b/transcriptclean.wdl
index 6e0de8a..1eea686 100644
--- a/transcriptclean.wdl
+++ b/transcriptclean.wdl
@@ -68,7 +68,7 @@ task GetSJsFromGtf {
task GetTranscriptCleanStats {
input {
- File transcriptCleanSamFile
+ File inputSam
String outputPrefix
String memory = "4G"
@@ -80,7 +80,7 @@ task GetTranscriptCleanStats {
set -e
mkdir -p "$(dirname ~{outputPrefix})"
get_TranscriptClean_stats \
- ~{transcriptCleanSamFile} \
+ ~{inputSam} \
~{outputPrefix}
}
@@ -96,7 +96,7 @@ task GetTranscriptCleanStats {
parameter_meta {
# inputs
- transcriptCleanSamFile: {description: "Output sam file from transcriptclean", category: "required"}
+ inputSam: {description: "Output sam file from transcriptclean", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
@@ -157,7 +157,7 @@ task TranscriptClean {
output {
File fastaFile = outputPrefix + "_clean.fa"
File logFile = outputPrefix + "_clean.log"
- File samFile = outputPrefix + "_clean.sam"
+ File outputSam = outputPrefix + "_clean.sam"
File logFileTE = outputPrefix + "_clean.TE.log"
}
@@ -194,7 +194,7 @@ task TranscriptClean {
# outputs
fastaFile: {description: "Fasta file containing corrected reads."}
logFile: {description: "Log file of transcriptclean run."}
- samFile: {description: "Sam file containing corrected aligned reads."}
+ outputSam: {description: "Sam file containing corrected aligned reads."}
logFileTE: {description: "TE log file of transcriptclean run."}
}
}
--
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