From 8495de6156e96c2e0c4ecbfe77f2a9456134c666 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 10 Jan 2020 11:16:11 +0100
Subject: [PATCH] add parameter_meta to biowdl input converter and YamltoJson
---
biowdl.wdl | 13 +++++++++++++
common.wdl | 7 +++++++
2 files changed, 20 insertions(+)
diff --git a/biowdl.wdl b/biowdl.wdl
index 32fd5a7..7aa68b2 100644
--- a/biowdl.wdl
+++ b/biowdl.wdl
@@ -52,4 +52,17 @@ task InputConverter {
runtime {
docker: dockerImage
}
+
+ parameter_meta {
+ samplesheet: {description: "The samplesheet to be processed.", category: "required"}
+ outputFile: {description: "The location the JSON representation of the samplesheet should be written to.",
+ category: "advanced"}
+ skipFileCheck: {description: "Whether or not the existance of the files mentioned in the samplesheet should be checked.",
+ category: "advanced"}
+ checkFileMd5sums: {description: "Whether or not the MD5 sums of the files mentioned in the samplesheet should be checked.",
+ category: "advanced"}
+ old: {description: "Whether or not the old samplesheet format should be used.", 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"}
+ }
}
diff --git a/common.wdl b/common.wdl
index f8b2cd8..73325bf 100644
--- a/common.wdl
+++ b/common.wdl
@@ -184,6 +184,13 @@ task YamlToJson {
runtime {
docker: dockerImage
}
+
+ parameter_meta {
+ yaml: {description: "The YAML file to convert.", category: "required"}
+ outputJson: {description: "The location the output JSON file should be written to.", 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"}
+ }
}
struct Reference {
--
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