first commit

defaults

+{
+  "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/NIST/",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "disk_size": "200",
+  "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
+  "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/NIST/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed",
+  "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "filtered_bed":"oss://pgx-result/renluyao/manuscript_v3.0/NIST/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed"
+}
+

inputs

+
+{
+  "{{ project_name }}.benchmarking_dir": "{{ benchmarking_dir }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.vcf": "{{ vcf }}",
+  "{{ project_name }}.BENCHMARKdocker": "{{ BENCHMARKdocker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.SMALLcluster_config": "{{ SMALLcluster_config }}",
+  "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
+  "{{ project_name }}.filtered_bed": "{{ filtered_bed }}",
+  "{{ project_name }}.BIGcluster_config": "{{ BIGcluster_config }}",
+  "{{ project_name }}.benchmark_region": "{{ benchmark_region }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+}

tasks/benchmark.wdl

+task benchmark {
+
+	File vcf
+	File benchmarking_dir
+	File ref_dir
+	File filtered_bed
+	String sample
+	String fasta
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${ref_dir} /cromwell_root/tmp/
+		cp -r ${benchmarking_dir} /cromwell_root/tmp/
+
+		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
+
+
+		/opt/hap.py/bin/hap.py /cromwell_root/tmp/NIST/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf ${vcf} -f ${filtered_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gzip_vcf = "${sample}.vcf.gz"
+		File gzip_vcf_index = "${sample}.vcf.gz.tbi"
+		File roc_all_csv = "${sample}.roc.all.csv.gz"
+		File roc_indel = "${sample}.roc.Locations.INDEL.csv.gz"
+		File roc_indel_pass = "${sample}.roc.Locations.INDEL.PASS.csv.gz"
+		File roc_snp = "${sample}.roc.Locations.SNP.csv.gz"
+		File roc_snp_pass = "${sample}.roc.Locations.SNP.PASS.csv.gz"
+		File summary = "${sample}.summary.csv"
+		File extended = "${sample}.extended.csv"
+		File metrics = "${sample}.metrics.json.gz"
+	}
+}

workflow.wdl

+import "./tasks/benchmark.wdl" as benchmark
+
+workflow   {{ project_name }}     {
+	File vcf
+	File benchmarking_dir
+	File ref_dir
+	File filtered_bed
+	String sample
+	String fasta
+	String BENCHMARKdocker
+	String BIGcluster_config
+	String disk_size
+
+
+		call benchmark.benchmark as benchmark {
+			input:
+			vcf=vcf,
+			sample=sample,
+			benchmarking_dir=benchmarking_dir,
+			filtered_bed=filtered_bed,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}	
+}
+