From d76faa5a05528e6a74488b46a18bdfcd1a9402ea Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Fri, 17 Sep 2021 09:55:37 +0200
Subject: [PATCH] update bcftools.wdk
---
bcftools.wdl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index 0cbfdef..0738d15 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -290,7 +290,7 @@ task View {
input {
File inputFile
String outputPath = "output.vcf"
-
+ Boolean excludeUncalled = false
String? exclude
String? include
String memory = "256M"
@@ -304,8 +304,9 @@ task View {
set -e
mkdir -p "$(dirname ~{outputPath})"
bcftools view \
- ~{"--include " + include} \
~{"--exclude " + exclude} \
+ ~{"--include " + include} \
+ ~{true="--exclude-uncalled" false="" excludeUncalled} \
-o ~{outputPath} \
-O ~{true="z" false="v" compressed} \
~{inputFile}
@@ -330,6 +331,8 @@ task View {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
include: {description: "Select sites for which the expression is true (see man page for details).", category: "advanced"}
exclude: {description: "Exclude sites for which the expression is true (see man page for details).", category: "advanced"}
+ excludeUncalled: {description: "Exclude sites without a called genotype (see man page for details).", 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"}
--
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