first commit

inputs

@@ -6,15 +6,13 @@
   "{{ project_name }}.fastqscreen.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
   "{{ project_name }}.fastqc.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
   "{{ project_name }}.benchmark.disk_size": "150",
-  "{{ project_name }}.rtg.disk_size": "100",
   "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
-  "{{ project_name }}.rtg.cluster_config": "OnDemand ecs.sn1ne.2xlarge img-ubuntu-vpc",
-  "{{ project_name }}.benchmark.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/hap.py:latest",
+  "{{ project_name }}.benchmark.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
   "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
   "{{ project_name }}.rtg.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
-  "{{ project_name }}.fastq_screen_conf": "oss://chinese-quartet/quartet-storage-data/reference_data/fastq_screen.conf",
+  "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
   "{{ project_name }}.bamqc.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
   "{{ project_name }}.fastqscreen.disk_size": "100",
   "{{ project_name }}.bamqc.disk_size": "500",

tasks/bamqc.wdl

@@ -20,6 +20,9 @@ task bamqc {
 	}
 
 	output {
-		Array[File] qualimap = glob("result/*")
+		File genome_result = "result/genome_results.txt"
+		File pdf = "result/report.pdf"
+		Array[File] png = glob("reuslt/images_qualimapReport/*.png")
+		Array[File] txt = glob("result/raw_data_qualimapReport/*.txt")
 	}
 }

tasks/benchmark.wdl

@@ -1,9 +1,8 @@
 task benchmark {
-	File gzvcf
-	File gzvcf_index
+	File vcf
 	File benchmarking_dir
 	File ref_dir
-	String sample = basename(gzvcf,".vcf.gz")
+	String sample = basename(vcf,".vcf")
 	String sample_mark
 	String fasta
 	String docker
@@ -16,14 +15,18 @@ task benchmark {
 		set -e
 		nt=$(nproc)
 		export HGREF=/cromwell_inputs/*/reference_data/GRCh38.d1.vd1.fa
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${vcf} -c > ${sample}.rtg.vcf.gz
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
+
 		if [ ${sample_mark} == "LCL5" ];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${gzvcf} -f ${benchmarking_dir}/LCL5.bed.gz --threads $nt -o ${sample}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.bed.gz --threads $nt -o ${sample}
 	    elif [ ${sample_mark} == "LCL6" ]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${gzvcf} -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
         elif [ ${sample_mark} == "LCL7" ]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${gzvcf} -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
 	    elif [ ${sample_mark} == "LCL8" ]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${gzvcf} -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
         else
         	echo "only for quartet samples"
         fi		

tasks/fastqscreen.wdl

@@ -13,6 +13,8 @@ task fastq_screen {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${screen_ref_dir} /cromwell_root/tmp/
 		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
 		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
 	>>>

tasks/zipindexVCF.wdl

@@ -1,23 +0,0 @@
-task rtg {
-	File vcf
-	String sample = basename(vcf,".vcf")
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		rtg bgzip ${vcf} -c > ${sample}.vcf.gz
-		rtg index -f vcf ${sample}.vcf.gz
-	>>>
-
-	runtime {
-		docker:docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File vcf_gz = "${sample}.vcf.gz"
-		File vcf_index = "${sample}.vcf.gz.tbi"
-	}
-}

workflow.wdl

@@ -1,7 +1,6 @@
 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/bamqc.wdl" as bamqc
-import "./tasks/zipindexVCF.wdl" as rtg
 import "./tasks/benchmark.wdl" as benchmark
 
 workflow {{ project_name }} {
@@ -35,15 +34,9 @@ workflow {{ project_name }} {
 			bai=sample[3]
 		}
 
-		call rtg.rtg as rtg {
-			input:
-			vcf=sample[4]
-		}
-
 		call benchmark.benchmark as benchmark {
 			input:
-			gzvcf=rtg.vcf_gz,
-			gzvcf_index=rtg.vcf_index,
+			vcf=sample[4],
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
 			sample_mark=sample[5],