From 91a5cdd20b1efd5b9955c4b03c72372a80e900e7 Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Wed, 12 Feb 2020 15:30:10 +0100
Subject: [PATCH] add default outputPath
---
bcftools.wdl | 2 +-
clever.wdl | 4 ++--
delly.wdl | 2 +-
manta.wdl | 2 +-
picard.wdl | 3 +--
survivor.wdl | 2 +-
6 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index d0837ec..866a310 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -25,7 +25,7 @@ version 1.0
task Bcf2Vcf {
input {
File bcf
- String outputPath
+ String outputPath = "./bcftools/SV.vcf"
String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
}
diff --git a/clever.wdl b/clever.wdl
index 3e7241e..ca28336 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -30,7 +30,7 @@ task Mateclever {
File indexedFiteredBam
BwaIndex bwaIndex
File predictions
- String outputPath
+ String outputPath = "./clever"
Int cleverMaxDelLength = 100000
Int maxLengthDiff= 30
Int maxOffset = 150
@@ -84,7 +84,7 @@ task Prediction {
File bamFile
File bamIndex
BwaIndex bwaIndex
- String outputPath
+ String outputPath = "./clever"
Int threads = 10
String memory = "15G"
diff --git a/delly.wdl b/delly.wdl
index 675a071..fab0637 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -28,7 +28,7 @@ task CallSV {
File bamIndex
File referenceFasta
File referenceFastaFai
- String outputPath
+ String outputPath = "./delly/delly.vcf"
String memory = "15G"
String dockerImage = "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
diff --git a/manta.wdl b/manta.wdl
index b7fbc4e..cd869bb 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -26,7 +26,7 @@ task Germline {
File bamIndex
File referenceFasta
File referenceFastaFai
- String runDir
+ String runDir = "./manta_run"
File? callRegions
File? callRegionsIndex
Boolean exome = false
diff --git a/picard.wdl b/picard.wdl
index 4b07f52..88ea3a2 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -642,9 +642,8 @@ task SortVcf {
task RenameSample {
input {
File inputVcf
- String outputPath
+ String outputPath = "./picard/renamed.vcf"
String newSampleName
-
String memory = "24G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.19.0--0"
diff --git a/survivor.wdl b/survivor.wdl
index fba613e..15bff09 100644
--- a/survivor.wdl
+++ b/survivor.wdl
@@ -31,7 +31,7 @@ task Merge {
Int strandType = 1
Int distanceBySvSize = 0
Int minSize = 30
- String outputPath
+ String outputPath = "./survivor/merged.vcf"
String memory = "24G"
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
}
--
GitLab