first commit

inputs

+{
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "400",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:3.8-1",
+  "{{ project_name }}.bam_index": "{{ bam_index }}",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

tasks/CallableLoci.wdl

+task CallableLoci {
+	
+	File bam
+	File bam_index
+	File ref_dir
+	String fasta
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+		set -o pipefail
+		set -e
+		java -jar GenomeAnalysisTK.jar \
+		-T CallableLoci \
+		-R ${ref_dir}/${fasta} \
+		-I ${bam} \
+		--maxDepth 300 \
+		--maxFractionOfReadsWithLowMAPQ 0.1 \
+		--maxLowMAPQ 1 \
+		--minBaseQuality 20 \
+		--minMappingQuality 20 \
+		--minDepth 10 \
+		--minDepthForLowMAPQ 10 \
+		-summary ${sample}_table.txt \
+		-o ${sample}_callable_status.bed
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File summary = "${sample}_table.txt"
+		File bed = "${sample}_callable_status.bed"
+	}
+}
+
+
+
+

workflow.wdl

+import "./tasks/CallableLoci.wdl" as CallableLoci
+
+workflow project_name {
+
+	File bam
+	File bam_index
+	File ref_dir
+	String fasta
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+	call CallableLoci.CallableLoci as CallableLoci {
+		input: 
+		bam=bam,
+		bam_index=bam_index,
+		ref_dir=ref_dir,
+		fasta=fasta,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+	}
+