docker

defaults

@@ -1,8 +1,8 @@
 {
   "fasta": "GRCh38.d1.vd1.fa",
   "disk_size": "500",
-  "cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-  "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
+  "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/manta:1.6.0",
   "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "memory": "64"
+  "memory": "30"
 }

tasks/manta.wdl

@@ -17,9 +17,7 @@ task manta {
 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
 
-		manta_config=opt/manta-1.6.0.centos6_x86_64/bin/configManta.py
-
-		$manta_config --normalBam ${normal_bam} --tumorBam ${tumour_bam} --referenceFasta ${ref_dir}/${fasta} --runDir /cromwell_root/tmp
+		/opt/manta-1.6.0.centos6_x86_64/bin/configManta.py --normalBam ${normal_bam} --tumorBam ${tumour_bam} --referenceFasta ${ref_dir}/${fasta} --runDir /cromwell_root/tmp
 
 		/cromwell_root/tmp/runWorkflow.py -j $nt -g ${memory}