From ca452303add0b2afeabb6595e09c7a036df58fc3 Mon Sep 17 00:00:00 2001
From: tomkuipers1402 <t.b.kuipers@outlook.com>
Date: Mon, 28 Dec 2020 10:31:34 +0100
Subject: [PATCH] annotation update
---
prepareShiny.wdl | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/prepareShiny.wdl b/prepareShiny.wdl
index 81354a1..13cd0b1 100644
--- a/prepareShiny.wdl
+++ b/prepareShiny.wdl
@@ -28,15 +28,15 @@ task CreateDesignMatrix {
Int threads = 1
String memory = "5G"
Int timeMinutes = 30
- String dockerImage = "quay.io/biocontainers/predex:0.9.1--pyh3252c3a_0"
+ String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
}
command {
set -e
mkdir -p ~{shinyDir}
predex design \
- -i ~{countTable} \
- -o ~{shinyDir}
+ --input ~{countTable} \
+ --output ~{shinyDir}
}
output {
@@ -70,19 +70,19 @@ task CreateAnnotation {
File referenceGtfFile
String shinyDir = "."
- Int threads = 1
- String memory = "10G"
- Int timeMinutes = 90
- String dockerImage = "quay.io/biocontainers/predex:0.9.1--pyh3252c3a_0"
+ Int threads = 2
+ String memory = "5G"
+ Int timeMinutes = 30
+ String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
}
command {
set -e
mkdir -p ~{shinyDir}
predex annotation \
- -f ~{referenceFasta} \
- -g ~{referenceGtfFile} \
- -o ~{shinyDir}
+ --fasta ~{referenceFasta} \
+ --gtf ~{referenceGtfFile} \
+ --output ~{shinyDir}
}
output {
--
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