From 9ec5ab9d38bf62aa074415cc7f717be53ff4ba09 Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Tue, 11 Feb 2020 16:15:01 +0100
Subject: [PATCH] add missing parameter_meta
---
bcftools.wdl | 7 ++++++-
samtools.wdl | 8 +++++++-
2 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index fbc3639..7c85c96 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -4,7 +4,6 @@ task Bcf2Vcf {
input {
File bcf
String outputPath
-
String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
}
@@ -21,4 +20,10 @@ task Bcf2Vcf {
runtime {
docker: dockerImage
}
+
+ parameter_meta {
+ bcf: {description: "The generated BCF from an SV caller", category: "advanced"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ 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/samtools.wdl b/samtools.wdl
index ac8fedf..a07657b 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -381,7 +381,6 @@ task FilterShortReadsBam {
File bamFile
String outputPathBam
String outputPathBamIndex
-
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
@@ -402,4 +401,11 @@ task FilterShortReadsBam {
runtime {
docker: dockerImage
}
+
+ parameter_meta {
+ bamFile: {description: "The bam file to process.", category: "required"}
+ outputPathBam: {description: "The filtered bam file.", category: "advanced"}
+ outputPathBamIndex: {description: "The index of filtered bam file.", 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"}
+ }
}
--
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