output of bamqc to multiqc

README.md

@@ -29,5 +29,7 @@
 
 (5) multiqc
 
+(6) VcfStats
 
+注：可查询multiqc支持的指控模块，按需求添加 <https://multiqc.info/docs/#multiqc-modules>
 

inputs

@@ -1,20 +1,26 @@
 {
   "{{ project_name }}.benchmarking_dir": "oss://chinese-quartet/quartet-result-data/NCTR_benchmarking_20181215/",
+  "{{ project_name }}.vcfstat.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.fastqc.disk_size": "150",
   "{{ project_name }}.benchmark.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
   "{{ 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 }}.vcfstat.disk_size": "100",
   "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
   "{{ 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 }}.mergeNum.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
   "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "{{ project_name }}.mergeNum.disk_size": "100",
   "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
   "{{ project_name }}.multiqc.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
   "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
+  "{{ project_name }}.mergeNum.cluster_config": "OnDemand ecs.sn1ne.xlarge img-ubuntu-vpc",
   "{{ project_name }}.bamqc.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
+  "{{ project_name }}.vcfstat.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
   "{{ project_name }}.fastqscreen.disk_size": "100",
   "{{ project_name }}.bamqc.disk_size": "500",
   "{{ project_name }}.multiqc.disk_size": "100",

tasks/bamqc.wdl

@@ -10,8 +10,8 @@ task bamqc {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir result --java-mem-size=32G 
-		tar -zcvf ${bamname}_qualimap.zip ./result
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G 
+		tar -zcvf ${bamname}_qualimap.zip ${bamname}
 	>>>
 
 	runtime {

tasks/mergeNum.wdl

@@ -0,0 +1,26 @@
+task mergeNum {
+	Array[File] vcfnumber
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		for i in ${seq=" " vcfnumber}
+		do
+		  cat $i | cut -d':' -f2 | tr '\n' '\t' | sed s'/\t$/\n/g' >> vcfstats
+		done
+		sed '1i\File\tFailed Filters\tPassed Filters\tSNPs\tMNPs\tInsertions\tDeletions\tIndels\tSame as reference\tSNP Transitions/Transversions\tTotal Het/Hom ratio\tSNP Het/Hom ratio\tMNP Het/Hom ratio\tInsertion Het/Hom ratio\tDeletion Het/Hom ratio\tIndel Het/Hom ratio\tInsertion/Deletion ratio\tIndel/SNP+MNP ratio' vcfstats > vcfstats.txt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcfstat="vcfstats.txt"
+	}
+}

tasks/multiqc.wdl

@@ -6,11 +6,7 @@ task multiqc {
 	Array[File] txt1
 	Array[File] txt2
 
-	Array[File] genome_result
-	Array[File] coverage
-	Array[File] insert_size
-	Array[File] genome_fraction
-	Array[File] gc_dist
+	Array[File] zip
 
 	Array[File] summary
 
@@ -28,8 +24,12 @@ task multiqc {
 
 		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-		cp ${sep=" " genome_result} ${sep=" " coverage} ${sep=" " insert_size} ${sep=" " genome_fraction} ${sep=" " gc_dist} /cromwell_root/tmp/bamqc
+		cp ${sep=" " zip} /cromwell_root/tmp/bamqc
 		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
+		for i in `ls /cromwell_root/tmp/bamqc`
+		do
+		  tar -zxvf $i
+		done
 
 		multiqc /cromwell_root/tmp/
 		ls > filelist

tasks/vcfstat.wdl

@@ -0,0 +1,22 @@
+task vcfstat {
+	File vcf
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		rtg vcfstats ${vcf} > onestats.txt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcfnumber="onestats.txt"
+	}
+}

workflow.wdl

@@ -3,6 +3,9 @@ import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/bamqc.wdl" as bamqc
 import "./tasks/benchmark.wdl" as benchmark
 import "./tasks/multiqc.wdl" as multiqc
+import "./tasks/vcfstat.wdl" as vcfstat
+import "./tasks/mergeNum.wdl" as mergeNum
+
 
 workflow {{ project_name }} {
 
@@ -43,6 +46,13 @@ workflow {{ project_name }} {
 			sample_mark=sample[5],
 			fasta=fasta
 		}
+
+		call vcfstat.vcfstat as vcfstat {
+			input:
+			vcf=sample[4]
+		}
+
+
 	}
 	call multiqc.multiqc as multiqc {
 		input:
@@ -50,13 +60,14 @@ workflow {{ project_name }} {
 		read2_zip=fastqc.read2_zip,
 		txt1=fastqscreen.txt1,
 		txt2=fastqscreen.txt2,
-		genome_result=bamqc.genome_result,
-		coverage=bamqc.coverage,
-		insert_size=bamqc.insert_size,
-		genome_fraction=bamqc.genome_fraction,
-		gc_dist=bamqc.gc_dist,
+		zip=bamqc.zip,
 		summary=benchmark.summary
 	}
 
+	call mergeNum.mergeNum as mergeNum {
+		input:
+		vcfnumber=vcfstat.vcfnumber
+	}
+
 }