From fcd32243e1aaa62a842435e5cc2671843d8afc54 Mon Sep 17 00:00:00 2001
From: tomkuipers1402 <t.b.kuipers@outlook.com>
Date: Thu, 24 Dec 2020 13:12:23 +0100
Subject: [PATCH] style update
---
prepareShiny.wdl | 34 +++++++++++++++++++---------------
1 file changed, 19 insertions(+), 15 deletions(-)
diff --git a/prepareShiny.wdl b/prepareShiny.wdl
index d304798..81354a1 100644
--- a/prepareShiny.wdl
+++ b/prepareShiny.wdl
@@ -33,10 +33,10 @@ task CreateDesignMatrix {
command {
set -e
- mkdir -p ${shinyDir}
+ mkdir -p ~{shinyDir}
predex design \
- -i ${countTable} \
- -o ${shinyDir}
+ -i ~{countTable} \
+ -o ~{shinyDir}
}
output {
@@ -51,14 +51,16 @@ task CreateDesignMatrix {
}
parameter_meta {
+ # inputs
countTable: {description: "The created count table from HTseq.", category: "required"}
- shinyDir: {description: "The directory to write the output to.", category: "required"}
-
+ shinyDir: {description: "The directory to write the output to.", category: "required"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ dgeDesign: {description: "Design matrix template to add sample information for DGE analysis."}
}
}
@@ -76,11 +78,11 @@ task CreateAnnotation {
command {
set -e
- mkdir -p ${shinyDir}
+ mkdir -p ~{shinyDir}
predex annotation \
- -f ${referenceFasta} \
- -g ${referenceGtfFile} \
- -o ${shinyDir}
+ -f ~{referenceFasta} \
+ -g ~{referenceGtfFile} \
+ -o ~{shinyDir}
}
output {
@@ -95,14 +97,16 @@ task CreateAnnotation {
}
parameter_meta {
+ # inputs
referenceFasta: {description: "The reference Fasta file.", category: "required"}
referenceGtfFile: {description: "The reference GTF file.", category: "required"}
- shinyDir: {description: "The directory to write the output to.", category: "required"}
-
+ shinyDir: {description: "The directory to write the output to.", category: "required"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
- category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ # outputs
+ dgeAnnotation: {description: "Annotation file for DGE analysis."}
}
}
--
GitLab