first commit

inputs

+{
+  "{{ project_name }}.Dedup_bam": "{{ Dedup_bam }}",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.ref_fa_fai": "GRCh38.d1.vd1.fa.fai",
+  "{{ project_name }}.FBdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/freebayes:1.2.0",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
+  "{{ project_name }}.Dedup_bam_index": "{{ Dedup_bam_index }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

tasks/Freebayes.wdl

+task Freebayes {
+
+    File ref_dir
+    File ref_fa_fai
+	String fasta
+
+	File Dedup_bam
+	File Dedup_bam_index
+	String sample
+	String FBdocker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		nt=$(nproc)
+		freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100) $nt -f ${ref_dir}/${fasta} --genotype-qualities ${Dedup_bam} > ${sample}_fb.vcf
+	>>>
+
+	runtime {
+		docker:FBdocker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcf = "${sample}_fb.vcf"
+	}
+}

workflow.wdl

+import "./tasks/Freebayes.wdl" as Freebayes
+
+
+workflow {{ project_name }} {
+
+	String sample
+	String FBdocker
+	File ref_fa_fai
+	String fasta
+	File Dedup_bam
+	File Dedup_bam_index
+	File ref_dir
+	String disk_size
+	String cluster_config
+
+	call Freebayes.Freebayes as Freebayes {
+		input:
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup_bam,
+		Dedup_bam_index=Dedup_bam_index,
+		sample=sample,
+		FBdocker=FBdocker,
+		cluster_config=cluster_config,
+		disk_size=disk_size,
+		ref_fa_fai=ref_fa_fai
+	}
+	}
+