read me

README.md

 vbt mendelian -ref <fasta_file> -mother <family_merged_vcf> -father <family_merged_vcf> -child <family_merged_vcf> -pedigree <ped_file> -outDir <output_directory> -out-prefix <output_directory_prefix> --output-violation-regions -thread-count <threads>
 ```
 
+## App输入文件
+
+```bash
+choppy samples WGS_germline_datapotal-latest --output samples
+```
+
+####Samples文件的输入包括
+
+**inputSamplesFile**
+
+```bash
+#read1	#read2	#sample_name
+```
+
+read1 是阿里云上fastq read1的地址
+
+read2 是阿里云上fastq read2的地址
+
+sample_name是指样本的命名
+
+所有上传的文件应有规范的命名
+
+Quartet_DNA_SequenceTech_SequenceMachine_SequenceSite_Sample_Replicate_Date.R1/R2.fastq.gz
+
+SequenceTech是指测序平台，如ILM、BGI等
+
+SequenceMachine是指测序仪器，如XTen、Nova、Hiseq（Illumina）、SEQ500、SEQ1000（BGI）等
+
+SequenceSite是指测序单位的英文缩写
+
+Sample是指LCL5、LCL6、LCL7、LCL8
+
+Replicate是指技术重复，从1开始依次增加
+
+Date是指数据获得日期，格式为20200710
+
+后缀一定是R1/R2.fastq.gz，不可以随意更改，R1/R2不可以写成r1/r2，fastq.gz不可以写成fq.gz
+
+各个缩写规范请见 https://fudan-pgx.yuque.com/docs/share/5baa851b-da97-47b9-b6c4-78f2b60595ab?# 《数据命名规范》
+
+**project**
+
+这个项目的名称，可以写自己可以识别的字符串，只能写英文和数字，不可以写中文
+
+#### Quartet样本的组合问题
+
+##### 1. 没有测LCL5和LCL6，或者没有同时测LCL5和LCL6
+
+只给出原始数据质控、比对数据质控、与标准集的比较
+
+##### 2. 包含LCL5和LCL6同卵双胞胎的数据，但是父母的数据不全
+
+只给出原始数据质控、比对数据质控、与标准集的比较、同卵双胞胎一致性
+
+##### 3. 四个quartet样本都测了
+
+给出所有结果原始数据质控、比对数据质控、与标准集的比较、同卵双胞胎一致性，符合孟德尔遗传比例
+
+**注意**：本app假设每个批次测的技术重复都一样，如batch 1测了LCL5、LCL6、LCL7和LCL8，batch 2 和batch 3也都测了这四个样本。本app不解决特别复杂的问题，例如batch1测了LCL5，LCL6，batch2测了LCL7和LCL8，本app只能给出原始数据质控、比对数据质控、与标准集的比较，不会把多个批次的数据合并计算孟德尔符合率和姐妹一致性。
+
 ## App输出文件
 
-本计算会产生大量的中间结果，这里说明最后整合好的结果文件，一共5个文件。
+本计算会产生大量的中间结果，这里说明最后整合好的结果文件，上述的三种情况得到的结果文件如下。
 
-####1. 原始数据质量控制
+###1. 没有测LCL5和LCL6，或者没有同时测LCL5和LCL6
+
+####1.1 原始数据质量控制
+
+####1.2 比对后数据质量控制
+
+##### 输出目录
+
+extract_multiqc
+
+##### 输出结果文件
+
+qualimap.final.result.txt
+
+####1.3 突变检出数据质量控制
+
+#####与标准集进行比较
+
+######输出目录
+
+extract_multiqc
+
+######输出结果文件
+
+benchmark.final.result.txt
+
+###2. 包含LCL5和LCL6同卵双胞胎的数据，但是父母的数据不全
+
+#### 2.1 原始数据质量控制
 
 ##### 输出目录
 
 
 fastqscreen.final.result.txt
 
-####2. 比对后数据质量控制
+#### 2.2 比对后数据质量控制
 
 ##### 输出目录
 
 
 qualimap.final.result.txt
 
-####3. 突变检出数据质量控制
+#### 2.3 突变检出数据质量控制
 
-#####3.1 与标准集进行比较
+##### 2.3.1 与标准集进行比较
 
-######输出目录
+#####输出目录
 
 extract_multiqc
 
-######输出结果文件
+#####输出结果文件
 
 benchmark.final.result.txt
 
-##### 3.2 通过Quartet家系设计
+**2.3.2** **姐妹一致性**
+
+##### 输出目录
+
+D5_D6
+
+##### 输出结果文件
+
+${project}.sister.txt
+
+### 3. 四个quartet样本都测了
+
+#### 3.1 原始数据质量控制
+
+##### 输出目录
+
+extract_multiqc
+
+##### 输出结果文件
+
+fastqc.final.result.txt
+
+fastqscreen.final.result.txt
+
+#### 3.2 比对后数据质量控制
+
+##### 输出目录
+
+extract_multiqc
+
+##### 输出结果文件
+
+qualimap.final.result.txt
+
+#### 3.3 突变检出数据质量控制
+
+##### 3.3.1 与标准集进行比较
+
+###### 输出目录
+
+extract_multiqc
+
+###### 输出结果文件
+
+benchmark.final.result.txt
+
+##### 3.3.2 通过Quartet家系设计
 
 ###### 输出目录
 
 | Precision | 查准率 |
 | Recall    | 查全率 |
 
-#####3.2 Quartet家系关系评估 ${project}.mendelian.txt
+##### 3.2 姐妹一致性 ${project}.sister.txt （样本没有没有测全，但是同时测了LCL5和LCL6）
+
+| 列名                  | 说明                                                         |
+| --------------------- | ------------------------------------------------------------ |
+| Family                | 家庭名字，我们目前的设计是4个Quartet样本，每个三个技术重复，family_1是指rep1的4个样本组成的家庭单位，以此类推。 |
+| Reproducibility_D5_D6 | Quartet-D5和Quartet-D6的一致性                               |
+
+#####3.3 Quartet家系关系评估 ${project}.mendelian.txt
 
 | 列名                          | 说明                                                         |
 | ----------------------------- | ------------------------------------------------------------ |

codescripts/D5_D6.py

+from __future__ import division
+import pandas as pd
+import sys, argparse, os
+
+
+# input arguments
+parser = argparse.ArgumentParser(description="this script is to calculate reproducibility between Quartet_D5 and Quartet_D6s")
+
+parser.add_argument('-sister', '--sister', type=str, help='sister.txt',  required=True)
+parser.add_argument('-project', '--project', type=str, help='project name',  required=True)
+
+
+args = parser.parse_args()
+sister_file = args.sister
+project_name = args.project
+
+# output file
+output_name = project_name + '.sister.reproducibility.txt'
+
+output_file = open(output_name,'w')
+
+# input files
+sister_dat = pd.read_table(sister_file)
+
+sister_same = 0
+sister_diff = 0
+
+for row in sister_dat.itertuples():
+	# sister
+	if row[5] == row[6]:
+		if row[5] == './.':
+			mendelian = 'noInfo'
+			sister_count = "no"
+		elif row[5] == '0/0':
+			mendelian = 'Ref'
+			sister_count = "no"
+		else:
+			mendelian = '1'
+			sister_count = "yes_same"
+	else:
+		mendelian = '0'
+		if (row[5] == './.' or row[5] == '0/0') and (row[6] == './.' or row[6] == '0/0'):
+			sister_count = "no"
+		else:
+			sister_count = "yes_diff"
+	if sister_count == 'yes_same':
+		sister_same += 1
+	elif sister_count == 'yes_diff':
+		sister_diff += 1
+	else:
+		pass
+
+sister = sister_same/(sister_same + sister_diff)
+outcolumn =  'Project\tReproducibility_D5_D6\n'
+outResult = project_name + '\t' + str(sister)  + '\n'
+output_file.write(outcolumn)
+output_file.write(outResult)
+
+
+

codescripts/how_many_samples.py

+import pandas as pd
+import sys, argparse, os
+from operator import itemgetter
+
+parser = argparse.ArgumentParser(description="This script is to get how many samples")
+
+parser.add_argument('-sample', '--sample', type=str, help='quartet_sample',  required=True)
+parser.add_argument('-rep', '--rep', type=str, help='quartet_rep',  required=True)
+args = parser.parse_args()
+
+# Rename input:
+sample = args.sample
+rep = args.rep
+
+quartet_sample = pd.read_table(sample,header=None)
+quartet_sample = list(quartet_sample[0])
+quartet_rep = pd.read_table(rep.header=None)
+quartet_rep = quartet_rep[0]
+
+#tags
+sister_tag = 'false'
+quartet_tag = 'false'
+
+quartet_rep_unique = list(set(quartet_rep))
+
+single_rep = [i for i in range(len(quartet_rep)) if quartet_rep[i] == quartet_rep_unique[0]]
+single_batch_sample = itemgetter(*single_rep)(quartet_sample)
+
+num = len(single_batch_sample)
+if num == 1:
+	sister_tag = 'false'
+	quartet_tag = 'false'
+elif num == 2:
+	if set(single_batch_sample) == set(['LCL5','LCL6']):
+		sister_tag = 'true'
+		quartet_tag = 'false'
+elif num == 3:
+	if ('LCL5' in single_batch_sample) and ('LCL6' in single_batch_sample):
+		sister_tag = 'true'
+		quartet_tag = 'false'
+elif num == 4:
+	if set(single_batch_sample) == set(['LCL5','LCL6','LCL7','LCL8']):
+		sister_tag = 'false'
+		quartet_tag = 'true'
+
+sister_outfile = open('sister_tag','w')
+quartet_outfile = open('quartet_tag','w')
+
+sister_outfile.write(sister_tag)
+quartet_outfile.write(quartet_tag)

tasks/D5_D6.wdl

+ task D5_D6 {
+	Array[File] splited_vcf
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		mkdir -p /cromwell_root/tmp/vcf
+
+		cp ${sep=" " splited_vcf} /cromwell_root/tmp/vcf
+
+		for i in /cromwell_root/tmp/vcf/*vcf
+		do
+			for j in /cromwell_root/tmp/vcf/*vcf
+			do
+				sample_i=$(echo $i | cut -f7 -d_)
+				sample_j=$(echo $j | cut -f7 -d_)
+				rep_i=$(echo $i | cut -f8 -d_)
+				rep_j=$(echo $j | cut -f8 -d_)
+				if [[ $sample_i == "LCL5" ] && [ $sample_j == "LCL6" ] && [ $rep_i == $rep_j ]];then
+					cat $i | grep -v '##' | cut -f1,2,4,5,10 | cut -d ':' -f1 > LCL5.txt
+					cat $j | grep -v '##' | cut -f10 | cut -d ':' -f1 > LCL6.txt
+					paste LCL5.txt LCL6.txt > sister.txt
+					python /opt/D5_D6.py -sister sister.txt -project ${project}.$rep_i
+				fi
+			done
+		done
+
+		for i in *.reproducibility.txt
+		do
+		  cat $i |  sed -n '2,2p' >> sister.summary
+		done
+		sed '1i\Family\tReproducibility_D5_D6' sister.summary > ${project}.sister.txt
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		Array[File] sister_file = glob("*.reproducibility.txt")
+		File sister_summary = "${project}.sister.txt"
+	}
+}

tasks/TNscope.wdl

-task TNscope {
-
-	File ref_dir
-    File dbsnp_dir
-    
-
-	String SENTIEON_INSTALL_DIR
-	String tumor_name
-	String normal_name
-	String docker
-	String cluster_config
-
-	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
-	String dbsnp
-	String disk_size
-
-	
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNscope.TN.vcf
-		
-	>>>
-
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNscope_vcf= "${sample}.TNscope.TN.vcf"
-		File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
-	}
-
-}

tasks/TNseq.wdl

-task TNseq {
-	
-    File ref_dir
-    File dbsnp_dir
-
-	String SENTIEON_INSTALL_DIR
-	String tumor_name
-	String normal_name
-	String docker
-	String cluster_config
-
-	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
-	String dbsnp
-	String disk_size
-
-	
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNseq.TN.vcf
-		
-	>>>
-
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
-		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
-	}
-
-}
-
-

tasks/joint_variant_calling.wdl

-task joint_variant_calling {
-	
-	File merged_bed
-	String sample
-	String docker
-	String disk_size
-	String cluster_config
-	
-
-	command <<<
-		
-		sentieon driver -r REFERENCE --algo GVCFtyper -v s1_VARIANT_GVCF \ -v s2_VARIANT_GVCF -v s3_VARIANT_GVCF VARIANT_VCF
-
-		>>>
-
-		runtime {
-		docker:docker
-    	cluster:cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File consensus_bed = "${sample}.27consensus.bed"
-		File filtered_bed = "${sample}.filtered.bed"
-	}
-}
-
-
-
-

tasks/merge_family.wdl

+ task merge_family {
+	Array[File] splited_vcf
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		mkdir -p /cromwell_root/tmp/vcf
+
+		cp ${sep=" " splited_vcf} /cromwell_root/tmp/vcf
+
+		for a in /cromwell_root/tmp/vcf/*vcf
+		do
+			for b in /cromwell_root/tmp/vcf/*vcf
+			do
+				for c in /cromwell_root/tmp/vcf/*vcf
+				do
+					for d in /cromwell_root/tmp/vcf/*vcf
+					do
+						sample_a=$(echo $a | cut -f7 -d_)
+						sample_b=$(echo $b | cut -f7 -d_)
+						sample_c=$(echo $c | cut -f7 -d_)
+						sample_d=$(echo $d | cut -f7 -d_)
+						rep_a=$(echo $a | cut -f8 -d_)
+						rep_b=$(echo $b | cut -f8 -d_)
+						rep_c=$(echo $c | cut -f8 -d_)
+						rep_d=$(echo $d | cut -f8 -d_)
+						if [ $sample_a == "LCL5" ] && [ $sample_b == "LCL6" ] && [ $sample_c == "LCL7" ] && [ $sample_d == "LCL8" ] && [ $rep_a == $rep_b ] && [ $rep_c == $rep_d ] && [ $rep_b == $rep_c ];then
+							cat $a | grep -v '#' > LCL5.body
+							cat $b | grep -v '#' | cut -f 10 > LCL6.body
+							cat $c | grep -v '#' | cut -f 10 > LCL7.body
+							cat $d | grep -v '#' | cut -f 10 > LCL8.body
+							echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > header_name
+							cat $a | grep '##' | cat - header_name > header
+							paste LCL5.body LCL6.body LCL7.body LCL8.body > family.body
+							cat header family.body > ${project}.$rep_a.family.vcf
+						fi
+					done
+				done
+			done
+		done
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		Array[File] family_vcf = glob("*.family.vcf")
+	}
+}

tasks/merge_mendelian.wdl

 		cat ${D5_trio_vcf} | grep -v '##' > ${family_name}.D5.txt
 		cat ${D6_trio_vcf} | grep -v '##' > ${family_name}.D6.txt
 		cat ${family_vcf} | grep -v '##' | awk '
-    		BEGIN { OFS = "\t" }
-    		NF > 2 && FNR > 1 { 
-        		for ( i=9; i<=NF; i++ ) { 
-            		split($i,a,":") ;$i = a[1];
-        		} 
-    		} 
-    		{ print }
-			' > ${family_name}.consensus.txt
+		    BEGIN { OFS = "\t" }
+		    NF > 2 && FNR > 1 { 
+		        for ( i=9; i<=NF; i++ ) { 
+		            split($i,a,":") ;$i = a[1];
+		        } 
+		    } 
+		    { print }
+		' > ${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}
 	>>>
 
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File project_mendelian = "${family_name}.mendelian.txt"
-		File project_mendelian_summary = "${family_name}.mendelian.summary.txt"
+		File project_mendelian = "${family_name}.txt"
+		File project_mendelian_summary = "${family_name}.summary.txt"
 	}
 }

tasks/multiqc.wdl

 
 		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
+		cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
+		cat multiqc_data/multiqc_fastqc.txt > multiqc_fastqc.txt
+		cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
+		cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json
 	
 	>>>
 

tasks/split_gvcf_files.wdl

-task split_gvcf_files {
+ task split_gvcf_files {
 	File gvcf
 	String project
 	String docker
 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
 		cat header body.filtered > ${project}.filtered.g.vcf
 
-
 		for i in $(seq 10 $ncol);  do  cat ${project}.filtered.g.vcf | cut -f1-9,$i > $i.splited.vcf; done
 
 		ls *splited.vcf | sort -n | paste - name > rename
 		cat rename | while read a b
 		do
 			mv $a $b.splited.vcf
-			if [[ $b.vcf =~ "LCL5_1" ]];then
-				cp $b.splited.vcf ${project}.LCL5_1.vcf
-		    elif [[ $b.vcf =~ "LCL5_2" ]]; then
-		    	cp $b.splited.vcf ${project}.LCL5_2.vcf
-	        elif [[ $b.vcf =~ "LCL5_3" ]]; then
-	        	cp $b.splited.vcf ${project}.LCL5_3.vcf
-		    elif [[ $b.vcf =~ "LCL6_1" ]]; then
-				cp $b.splited.vcf ${project}.LCL6_1.vcf
-		    elif [[ $b.vcf =~ "LCL6_2" ]]; then
-				cp $b.splited.vcf ${project}.LCL6_2.vcf
-		    elif [[ $b.vcf =~ "LCL6_3" ]]; then
-				cp $b.splited.vcf ${project}.LCL6_3.vcf
-		    elif [[ $b.vcf =~ "LCL7_1" ]]; then
-				cp $b.splited.vcf ${project}.LCL7_1.vcf
-		    elif [[ $b.vcf =~ "LCL7_2" ]]; then
-				cp $b.splited.vcf ${project}.LCL7_2.vcf
-		    elif [[ $b.vcf =~ "LCL7_3" ]]; then
-				cp $b.splited.vcf ${project}.LCL7_3.vcf
-		    elif [[ $b.vcf =~ "LCL8_1" ]]; then
-				cp $b.splited.vcf ${project}.LCL8_1.vcf
-		    elif [[ $b.vcf =~ "LCL8_2" ]]; then
-				cp $b.splited.vcf ${project}.LCL8_2.vcf
-		    elif [[ $b.vcf =~ "LCL8_3" ]]; then
-				cp $b.splited.vcf ${project}.LCL8_3.vcf
-	        fi
+			sample=$(echo $b | cut -f6 -d_)
+			rep=$(echo $b | cut -f7 -d_)
+			echo $sample >> quartet_sample
+			echo $rep >> quartet_rep
 		done
 
-        cat ${project}.LCL5_1.vcf | grep -v '#' > LCL5_1.body
-        cat ${project}.LCL5_2.vcf | grep -v '#' > LCL5_2.body
-        cat ${project}.LCL5_3.vcf | grep -v '#' > LCL5_3.body
-
-        cat ${project}.LCL6_1.vcf | grep -v '#' | cut -f 10 > LCL6_1.body
-        cat ${project}.LCL6_2.vcf | grep -v '#' | cut -f 10 > LCL6_2.body
-        cat ${project}.LCL6_3.vcf | grep -v '#' | cut -f 10 > LCL6_3.body
-
-        cat ${project}.LCL7_1.vcf | grep -v '#' | cut -f 10 > LCL7_1.body
-        cat ${project}.LCL7_2.vcf | grep -v '#' | cut -f 10 > LCL7_2.body
-        cat ${project}.LCL7_3.vcf | grep -v '#' | cut -f 10 > LCL7_3.body
-
-        cat ${project}.LCL8_1.vcf | grep -v '#' | cut -f 10 > LCL8_1.body
-        cat ${project}.LCL8_2.vcf | grep -v '#' | cut -f 10 > LCL8_2.body
-        cat ${project}.LCL8_3.vcf | grep -v '#' | cut -f 10 > LCL8_3.body
-
-		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > header_name
-
-		cat ${project}.LCL5_1.vcf | grep '##' | cat - header_name > header
-
-		paste LCL5_1.body LCL6_1.body LCL7_1.body LCL8_1.body > family_1.body
-		paste LCL5_2.body LCL6_2.body LCL7_2.body LCL8_2.body > family_2.body
-		paste LCL5_3.body LCL6_3.body LCL7_3.body LCL8_3.body > family_3.body
-
-		cat header family_1.body > ${project}.1.family.vcf
-		cat header family_2.body > ${project}.2.family.vcf
-		cat header family_3.body > ${project}.3.family.vcf
-
-
+		python /opt/how_many_samples.py -sample quartet_sample -rep quartet_rep
 
 
 	>>>
 	}
 	output {
 		Array[File] splited_vcf = glob("*.splited.vcf")
-		Array[File] family_vcf = glob("*.family.vcf")
-		File LCL5_1 = "${project}.LCL5_1.vcf"
-		File LCL5_2 = "${project}.LCL5_2.vcf"
-		File LCL5_3 = "${project}.LCL5_3.vcf"
-		File LCL6_1 = "${project}.LCL6_1.vcf"
-		File LCL6_2 = "${project}.LCL6_2.vcf"
-		File LCL6_3 = "${project}.LCL6_3.vcf"
-		File LCL7_1 = "${project}.LCL7_1.vcf"
-		File LCL7_2 = "${project}.LCL7_2.vcf"
-		File LCL7_3 = "${project}.LCL7_3.vcf"
-		File LCL8_1 = "${project}.LCL8_1.vcf"
-		File LCL8_2 = "${project}.LCL8_2.vcf"
-		File LCL8_3 = "${project}.LCL8_3.vcf"
+		File sister_tag = "sister_tag"
+		File quartet_tag = "quartet_tag"
 	}
 }

workflow.wdl

 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/extract_multiqc.wdl" as extract_multiqc
+import "./tasks/D5_D6.wdl" as D5_D6
+import "./tasks/merge_family.wdl" as merge_family
+
 
 workflow {{ project_name }} {
 
 	call split_gvcf_files.split_gvcf_files as split_gvcf_files {
 		input:
 		gvcf=GVCFtyper.gvcf,
-		docker=BENCHMARKdocker,
+		docker=DIYdocker,
 		project=project,
 		cluster_config=SMALLcluster_config,
 		disk_size=disk_size
 	}
 
+
 	Array[File] single_gvcf = split_gvcf_files.splited_vcf
 
 	scatter (idx in range(length(single_gvcf))) {
 		disk_size=disk_size
 	}
 
-	Array[File] family_vcfs = split_gvcf_files.family_vcf
+	Boolean sister_tag = read_boolean(split_gvcf_files.sister_tag)
+	Boolean quartet_tag = read_boolean(split_gvcf_files.quartet_tag)
 
-	scatter (idx in range(length(family_vcfs))) {
-		call mendelian.mendelian as mendelian {
+	if (sister_tag) {
+		call D5_D6.D5_D6 as D5_D6 {
 			input:
-			family_vcf=family_vcfs[idx],
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=MENDELIANdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size		
+			splited_vcf=split_gvcf_files.splited_vcf,
+			project=project,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size,
 		}
+	}
 
-		call merge_mendelian.merge_mendelian as merge_mendelian {
+	if (quartet_tag) {
+		call merge_family.merge_family as merge_family {
 			input:
-			D5_trio_vcf=mendelian.D5_trio_vcf,
-			D6_trio_vcf=mendelian.D6_trio_vcf,
-			family_vcf=family_vcfs[idx],
+			splited_vcf=split_gvcf_files.splited_vcf,
+			project=project,
 			docker=DIYdocker,
 			cluster_config=SMALLcluster_config,
-			disk_size=disk_size
+			disk_size=disk_size,
 		}
-	}
 
-	call quartet_mendelian.quartet_mendelian as quartet_mendelian {
-		input:
-		project_mendelian_summary=merge_mendelian.project_mendelian_summary,
-		project=project,
-		docker=DIYdocker,
-		cluster_config=SMALLcluster_config,
-		disk_size=disk_size
-	}
+		Array[File] family_vcfs = merge_family.family_vcf
+		scatter (idx in range(length(family_vcfs))) {
+			call mendelian.mendelian as mendelian {
+				input:
+				family_vcf=family_vcfs[idx],
+				ref_dir=ref_dir,
+				fasta=fasta,
+				docker=MENDELIANdocker,
+				cluster_config=BIGcluster_config,
+				disk_size=disk_size		
+			}
+
+			call merge_mendelian.merge_mendelian as merge_mendelian {
+				input:
+				D5_trio_vcf=mendelian.D5_trio_vcf,
+				D6_trio_vcf=mendelian.D6_trio_vcf,
+				family_vcf=family_vcfs[idx],
+				docker=DIYdocker,
+				cluster_config=SMALLcluster_config,
+				disk_size=disk_size
+			}
+		}
 
+		call quartet_mendelian.quartet_mendelian as quartet_mendelian {
+			input:
+			project_mendelian_summary=merge_mendelian.project_mendelian_summary,
+			project=project,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
+		}
+	}
 }