整理信息

codescripts/extract_multiqc.py

@@ -0,0 +1,65 @@
+import json
+import pandas as pd
+import sys, argparse, os
+
+parser = argparse.ArgumentParser(description="This script is to get information from multiqc")
+
+parser.add_argument('-fastqc_qualimap', '--fastqc_qualimap', type=str, help='multiqc_general_stats.txt',  required=True)
+parser.add_argument('-fastqc', '--fastqc', type=str, help='multiqc_fastqc.txt',  required=True)
+parser.add_argument('-fastqscreen', '--fastqscreen', type=str, help='multiqc_fastq_screen.txt',  required=True)
+parser.add_argument('-hap', '--happy', type=str, help='multiqc_happy_data.json',  required=True)
+
+args = parser.parse_args()
+
+# Rename input:
+fastqc_qualimap_file = args.fastqc_qualimap
+fastqc_file = args.fastqc
+fastqscreen_file = args.fastqscreen
+hap_file = args.happy
+
+
+# fastqc and qualimap
+dat = pd.read_table(fastqc_qualimap_file)
+
+fastqc = dat.loc[:, dat.columns.str.startswith('FastQC')]
+fastqc.insert(loc=0, column='Sample', value=dat['Sample'])
+fastqc_stat = fastqc.dropna()
+
+# qulimap
+qualimap = dat.loc[:, dat.columns.str.startswith('QualiMap')]
+qualimap.insert(loc=0, column='Sample', value=dat['Sample'])
+qualimap_stat = qualimap.dropna()
+
+# fastqc
+dat = pd.read_table(fastqc_file)
+
+fastqc_module = dat.loc[:, "per_base_sequence_quality":"kmer_content"]
+fastqc_module.insert(loc=0, column='Sample', value=dat['Sample'])
+fastqc_all = pd.merge(fastqc_stat,fastqc_module,  how='outer', left_on=['Sample'], right_on = ['Sample'])
+
+# fastqscreen
+dat = pd.read_table(fastqscreen_file)
+fastqscreen = dat.loc[:, dat.columns.str.endswith('percentage')]
+dat['Sample'] = [i.replace('_screen','') for i in dat['Sample']]
+fastqscreen.insert(loc=0, column='Sample', value=dat['Sample'])
+
+# benchmark
+with open(hap_file) as hap_json:
+	happy = json.load(hap_json)
+dat =pd.DataFrame.from_records(happy)
+dat = dat.loc[:, dat.columns.str.endswith('ALL')]
+dat_transposed = dat.T
+benchmark = dat_transposed.loc[:,['sample_id','METRIC.Precision','METRIC.Recall']]
+benchmark.columns = ['Sample','Precision','Recall']
+
+#output
+fastqc_all.to_csv('fastqc.final.result.txt',sep="\t",index=0)
+fastqscreen.to_csv('fastqscreen.final.result.txt',sep="\t",index=0)
+qualimap_stat.to_csv('qualimap.final.result.txt',sep="\t",index=0)
+benchmark.to_csv('benchmark.final.result.txt',sep="\t",index=0)
+
+
+
+
+
+

tasks/Haplotyper_gVCF.wdl

@@ -1,6 +1,5 @@
 task Haplotyper_gVCF {
 	
-	
     File ref_dir
 	String SENTIEON_INSTALL_DIR
 	String fasta

tasks/extract_multiqc.wdl

@@ -0,0 +1,29 @@
+task extract_multiqc {
+
+	File fastqc_qualimap
+	File fastqc
+	File fastqscreen
+	File hap
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		python /opt/extract_multiqc.py -fastqc_qualimap ${fastqc_qualimap} -fastqc ${fastqc} -fastqscreen ${fastqscreen} -hap ${hap}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File fastqc_result = "fastqc.final.result.txt"
+		File fastqscreen_result = "fastqscreen.final.result.txt"
+		File qualimap_result = "qualimap.final.result.txt"
+		File hap_result = "benchmark.final.result.txt"
+	}
+}

tasks/mendelian.wdl

@@ -1,8 +1,8 @@
 task mendelian {
 	File family_vcf
 	File ref_dir
+	String family_name = basename(family_vcf,".family.vcf")
 	String fasta
-	String project
 	String docker
 	String cluster_config
 	String disk_size
@@ -11,19 +11,19 @@ task mendelian {
 		export LD_LIBRARY_PATH=/opt/htslib-1.9
 		nt=$(nproc)
 
-		echo -e "${project}\tLCL8\t0\t0\t2\t-9\n${project}\tLCL7\t0\t0\t1\t-9\n${project}\tLCL5\tLCL7\tLCL8\t2\t-9" > ${project}.D5.ped
+		echo -e "${family_name}\tLCL8\t0\t0\t2\t-9\n${family_name}\tLCL7\t0\t0\t1\t-9\n${family_name}\tLCL5\tLCL7\tLCL8\t2\t-9" > ${family_name}.D5.ped
 
 		mkdir VBT_D5
-		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf} -father ${family_vcf} -child ${family_vcf} -pedigree ${project}.D5.ped -outDir VBT_D5 -out-prefix ${project}.D5 --output-violation-regions -thread-count $nt
+		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf} -father ${family_vcf} -child ${family_vcf} -pedigree ${family_name}.D5.ped -outDir VBT_D5 -out-prefix ${family_name}.D5 --output-violation-regions -thread-count $nt
 
-		cat VBT_D5/${project}.D5_trio.vcf > ${project}.D5.vcf
+		cat VBT_D5/${family_name}.D5_trio.vcf > ${family_name}.D5.vcf
 
-		echo -e "${project}\tLCL8\t0\t0\t2\t-9\n${project}\tLCL7\t0\t0\t1\t-9\n${project}\tLCL6\tLCL7\tLCL8\t2\t-9" > ${project}.D6.ped
+		echo -e "${family_name}\tLCL8\t0\t0\t2\t-9\n${family_name}\tLCL7\t0\t0\t1\t-9\n${family_name}\tLCL6\tLCL7\tLCL8\t2\t-9" > ${family_name}.D6.ped
 
 		mkdir VBT_D6
-		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf} -father ${family_vcf} -child ${family_vcf} -pedigree ${project}.D6.ped -outDir VBT_D6 -out-prefix ${project}.D6 --output-violation-regions -thread-count $nt
+		/opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf} -father ${family_vcf} -child ${family_vcf} -pedigree ${family_name}.D6.ped -outDir VBT_D6 -out-prefix ${family_name}.D6 --output-violation-regions -thread-count $nt
 
-		cat VBT_D6/${project}.D6_trio.vcf > ${project}.D6.vcf
+		cat VBT_D6/${family_name}.D6_trio.vcf > ${family_name}.D6.vcf
 	>>>
 
 	runtime {
@@ -33,13 +33,12 @@ task mendelian {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File D5_ped = "${project}.D5.ped"
-		File D6_ped = "${project}.D6.ped"
+		File D5_ped = "${family_name}.D5.ped"
+		File D6_ped = "${family_name}.D6.ped"
 		Array[File] D5_mendelian = glob("VBT_D5/*")
 		Array[File] D6_mendelian = glob("VBT_D6/*")
-		File D5_trio_vcf = "${project}.D5.vcf"
-		File D6_trio_vcf = "${project}.D6.vcf"
-		File family_all_vcf = "${project}.vcf"
+		File D5_trio_vcf = "${family_name}.D5.vcf"
+		File D6_trio_vcf = "${family_name}.D6.vcf"
 	}
 }
 

tasks/merge_mendelian.wdl

@@ -2,14 +2,14 @@ task merge_mendelian {
 	File D5_trio_vcf
 	File D6_trio_vcf
 	File family_vcf
-	String project
+	String family_name = basename(family_vcf,".family.vcf")
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		cat ${D5_trio_vcf} | grep -v '##' > ${project}.D5.txt
-		cat ${D6_trio_vcf} | grep -v '##' > ${project}.D6.txt
+		cat ${D5_trio_vcf} | grep -v '##' > ${family_name}.D5.txt
+		cat ${D6_trio_vcf} | grep -v '##' > ${family_name}.D6.txt
 		cat ${family_vcf} | grep -v '##' | awk '
     		BEGIN { OFS = "\t" }
     		NF > 2 && FNR > 1 { 
@@ -18,8 +18,8 @@ task merge_mendelian {
         		} 
     		} 
     		{ print }
-			' > ${project}.consensus.txt
-		python /opt/merge_two_family_with_genotype.py -LCL5 ${project}.D5.txt -LCL6 ${project}.D6.txt -genotype ${project}.consensus.txt -family ${project}.mendelian
+			' > ${family_name}.consensus.txt
+		python /opt/merge_two_family_with_genotype.py -LCL5 ${family_name}.D5.txt -LCL6 ${family_name}.D6.txt -genotype ${family_name}.consensus.txt -family ${family_name}
 	>>>
 
 	runtime {
@@ -29,7 +29,7 @@ task merge_mendelian {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File project_mendelian = "${project}.mendelian.txt"
-		File project_mendelian_summary = "${project}.mendelian.summary.txt"
+		File project_mendelian = "${family_name}.mendelian.txt"
+		File project_mendelian_summary = "${family_name}.mendelian.summary.txt"
 	}
 }

tasks/multiqc.wdl

@@ -30,6 +30,11 @@ task multiqc {
 		done
 
 		multiqc /cromwell_root/tmp/
+
+		cp multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
+		cp multiqc_data/multiqc_fastqc.txt > multiqc_fastqc.txt
+		cp multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
+		cp multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
 	
 	>>>
 
@@ -43,5 +48,9 @@ task multiqc {
 	output {
 		File multiqc_html = "multiqc_report.html"
 		Array[File] multiqc_txt = glob("multiqc_data/*")
+		File fastqc_qualimap = "multiqc_general_stats.txt"
+		File fastqc = "multiqc_fastqc.txt"
+		File fastqscreen = "multiqc_fastq_screen.txt"
+		File hap = "multiqc_happy_data.json"
 	}
 }

workflow.wdl

@@ -15,6 +15,7 @@ import "./tasks/quartet_mendelian.wdl" as quartet_mendelian
 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimap.wdl" as qualimap
+import "./tasks/extract_multiqc.wdl" as extract_multiqc
 
 workflow {{ project_name }} {
 
@@ -224,6 +225,17 @@ workflow {{ project_name }} {
 		disk_size=disk_size
 	}
 
+	call extract_multiqc.extract_multiqc as extract_multiqc {
+		input:
+		fastqc_qualimap=multiqc.fastqc_qualimap,
+		fastqc=multiqc.fastqc,
+		fastqscreen=multiqc.fastqscreen,
+		hap=multiqc.hap,
+		docker=DIYdocker,
+		cluster_config=SMALLcluster_config,
+		disk_size=disk_size
+	}
+
 	Array[File] family_vcfs = split_gvcf_files.family_vcf
 
 	scatter (idx in range(length(family_vcfs))) {
@@ -232,7 +244,6 @@ workflow {{ project_name }} {
 			family_vcf=family_vcfs[idx],
 			ref_dir=ref_dir,
 			fasta=fasta,
-			project=project,
 			docker=MENDELIANdocker,
 			cluster_config=BIGcluster_config,
 			disk_size=disk_size		
@@ -243,7 +254,6 @@ workflow {{ project_name }} {
 			D5_trio_vcf=mendelian.D5_trio_vcf,
 			D6_trio_vcf=mendelian.D6_trio_vcf,
 			family_vcf=family_vcfs[idx],
-			project=project,
 			docker=DIYdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size