From 5607a41d6073b2cfb0f182073eb63fc015042f3f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 20 Feb 2019 17:35:07 +0100
Subject: [PATCH] make output dirs
---
gatk.wdl | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index b2c268e..c354c7d 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -18,6 +18,7 @@ task ApplyBQSR {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputBamPath})
gatk --java-options -Xmx~{memory}G \
ApplyBQSR \
--create-output-bam-md5 \
@@ -69,6 +70,7 @@ task BaseRecalibrator {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{recalibrationReportPath})
gatk --java-options -Xmx~{memory}G \
BaseRecalibrator \
-R ~{reference.fasta} \
@@ -107,6 +109,7 @@ task CombineGVCFs {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
CombineGVCFs \
-R ~{reference.fasta} \
@@ -141,6 +144,7 @@ task GatherBqsrReports {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputReportPath})
gatk --java-options -Xmx~{memory}G \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
@@ -178,6 +182,7 @@ task GenotypeGVCFs {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
GenotypeGVCFs \
-R ~{reference.fasta} \
@@ -266,6 +271,7 @@ task MuTect2 {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputVcf})
gatk --java-options -Xmx~{memory}G \
Mutect2 \
-R ~{reference.fasta} \
@@ -303,6 +309,7 @@ task SplitNCigarReads {
command {
set -e -o pipefail
+ mkdir -p $(dirname ~{outputBam})
gatk --java-options -Xmx~{memory}G \
SplitNCigarReads \
-I ~{inputBam.file} \
--
GitLab