From bb6896686042d1c60e19ad4483bfd5bed255a617 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 3 Mar 2020 09:17:13 +0100
Subject: [PATCH] address review comments
---
gatk.wdl | 4 ++--
rtg.wdl | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 4029ae0..cd0ed18 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1393,8 +1393,8 @@ task SelectVariants {
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
selectTypeToInclude: {description: "Select only a certain type of variants from the input file", category: "common"}
- outputPath: {description: "The location the output VCF file should be written.", category: "required"}
- intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "advanced"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
diff --git a/rtg.wdl b/rtg.wdl
index 10856ee..b629b1d 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -51,7 +51,7 @@ task Format {
format: {description: "Format of input. Allowed values are [fasta, fastq, fastq-interleaved, sam-se, sam-pe] (Default is fasta)",
category: "advanced"}
outputPath: {description: "Where the output should be placed.", category: "advanced"}
- inputFiles: {description: "input sequence files. May be specified 1 or more times."}
+ inputFiles: {description: "input sequence files. May be specified 1 or more times.", category: "required"}
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"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
--
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