From 6fbe1b7f37f3705c93cbe9ad7542ab10e0278561 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 May 2020 16:09:19 +0200
Subject: [PATCH] Parameter meta for multiqc updated. Make sure data dir output
is always zipped by default.
---
multiqc.wdl | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/multiqc.wdl b/multiqc.wdl
index 62ca542..6a967b3 100644
--- a/multiqc.wdl
+++ b/multiqc.wdl
@@ -42,7 +42,7 @@ task MultiQC {
Array[String]+? module
Boolean dataDir = false
String? dataFormat
- Boolean zipDataDir = false
+ Boolean zipDataDir = true
Boolean export = false
Boolean flat = false
Boolean interactive = true
@@ -128,7 +128,7 @@ task MultiQC {
output {
File multiqcReport = outDir + "/" + reportFilename + "_report.html"
- File multiqcDataDir = outDir + "/" +reportFilename + "_data"
+ File? multiqcDataDirZip = outDir + "/" +reportFilename + "_data.zip"
}
runtime {
@@ -151,13 +151,11 @@ task MultiQC {
tag: {description: "Equivalent to MultiQC's `--tag` option.", category: "advanced"}
ignore: {description: "Equivalent to MultiQC's `--ignore` option.", category: "advanced"}
ignoreSamples: {description: "Equivalent to MultiQC's `--ignore-samples` option.", category: "advanced"}
- ignoreSymlinks: {description: "Equivalent to MultiQC's `--ignore-symlinks` flag.", category: "advanced"}
sampleNames: {description: "Equivalent to MultiQC's `--sample-names` option.", category: "advanced"}
fileList: {description: "Equivalent to MultiQC's `--file-list` option.", category: "advanced"}
exclude: {description: "Equivalent to MultiQC's `--exclude` option.", category: "advanced"}
module: {description: "Equivalent to MultiQC's `--module` option.", category: "advanced"}
- dataDir: {description: "Equivalent to MultiQC's `--data-dir` flag.", category: "advanced"}
- noDataDir: {description: "Equivalent to MultiQC's `--no-data-dir` flag.", category: "advanced"}
+ dataDir: {description: "Whether to output a data dir. Sets `--data-dir` or `--no-data-dir` flag.", category: "advanced"}
dataFormat: {description: "Equivalent to MultiQC's `--data-format` option.", category: "advanced"}
zipDataDir: {description: "Equivalent to MultiQC's `--zip-data-dir` flag.", category: "advanced"}
export: {description: "Equivalent to MultiQC's `--export` flag.", category: "advanced"}
@@ -168,8 +166,6 @@ task MultiQC {
megaQCUpload: {description: "Opposite to MultiQC's `--no-megaqc-upload` flag.", category: "advanced"}
config: {description: "Equivalent to MultiQC's `--config` option.", category: "advanced"}
clConfig: {description: "Equivalent to MultiQC's `--cl-config` option.", category: "advanced"}
- finished: {description: "An array of booleans that can be used to let multiqc wait on stuff.", category: "internal_use_only"}
-
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.",
--
GitLab