workflow pancancer_singlesample_umi{
	String normal
	String tumor
	String cancer
	String project = "624gene"
	String raw_bed = "/dataseq/jmdna/database/bed/624.merge.bed"
	String bed = "/dataseq/jmdna/database/bed/624plus20bp_merge.bed"
	String outputDir
	String inputDir	
	String ref = "/dataseq/jmdna/database/genome/hg19/hg19.fa"
	String codes_dir = "/dataseq/jmdna/codes/624"
	String accessBed = "/dataseq/jmdna/software/cnvkit-0.9.7/data/access-5k-mappable.hg19.bed"
	String annotateGene = "/dataseq/jmdna/software/cnvkit-0.9.7/data/refFlat.txt"
	String gc_wiggle = "/dataseq/jmdna/codes/pancancer_controlsample/hg19.gc200Base.txt.gz"
	#创建目录
	call create_dir{
		input:
            outputDir=outputDir
    }
	scatter (read in ["1","2"]){
		call changehead{
			input:
				newdir=create_dir.newdir,
				tumor=tumor,
				inputDir=inputDir,
				outputDir=outputDir,
				read=read
		}
	}
	
	call qc{
        input:
			data=changehead.outputFile,
            tumor=tumor,
            inputDir=inputDir,
            outputDir=outputDir,
            codes_dir=codes_dir
    }
	call qc_normal{
        input:
			data=changehead.outputFile,
            normal=normal,
            inputDir=inputDir,
            outputDir=outputDir			
    }
	scatter (name in [normal,tumor]){
		call alignment_bwa{
			input:
				name=name,
				outputDir=outputDir,
				ref=ref,
				qc_T=qc.outputFile,
				qc_N=qc_normal.outputFile
		}
		call rmdup{
			input:
				name=name,
				outputDir=outputDir,
				ref=ref,
				bam=alignment_bwa.sorted
		}
		call generater_mpileup{
			input:
				rmdup=rmdup.rmdup,
				name=name,
				ref=ref,
				bed=bed,
				outputDir=outputDir
		}
	}
	call mutation_calling{
        	input:
			tumor=tumor,
			outputDir=outputDir,	
			ref=ref,
			bed=bed,
			normal=normal,
			codes_dir=codes_dir,
			rmdup=rmdup.rmdup[1]
    }
	call mutation_calling_normal{
        	input:
			normal=normal,
			outputDir=outputDir,	
			ref=ref,
			bed=bed,
			rmdup=rmdup.rmdup[0]
    }
	call hotspot{
        	input:
				rmdupBam=rmdup.rmdup[1],
        		tumor=tumor,
	    		outputDir=outputDir,
	    		ref=ref,
	    		codes_dir=codes_dir
    }
	call annovar{
		input:
			codes_dir=codes_dir,
			tumor=tumor,
			normal=normal,
			outputDir=outputDir,
			tvcf=mutation_calling.vcf,
			nvcf=mutation_calling_normal.vcf
    }
	scatter (name in [normal,tumor]){
		call qc_2{
			input:
				ref=ref,
				bed=raw_bed,
				name=name,
				tumor=tumor,
				outputDir=outputDir,
				codes_dir=codes_dir,
				anno=annovar.anno
		}
	}
	call fusion{
			input:
				ref=ref,
				codes_dir=codes_dir,
				tumor=tumor,
				cancer=cancer,
				outputDir=outputDir,
				Bam=alignment_bwa.sorted[1],
				project=project
	}
	call TMB{
		input:
			codes_dir=codes_dir,
			tumor=tumor,
			outputDir=outputDir,
			anno=annovar.anno
	}
	call conpair{
		input:
			tumor=tumor,
			normal=normal,
			ref=ref,
			outputDir=outputDir,
			rmdupBam=rmdup.rmdup
	}
	call chemoTherapy{
		input:
			codes_dir=codes_dir,
			normal=normal,
			outputDir=outputDir,
			ref=ref,
			project=project,
			rmdupBam=rmdup.rmdup[0]
	}
	call tumor_content{
		input:
			ref=ref,
			tumor=tumor,
			normal=normal,
			outputDir=outputDir,
			gc_wiggle=gc_wiggle,
			codes_dir=codes_dir,
			pileup=generater_mpileup.pileup
	}
	call cnvkit{
			input:
				tumor=tumor,
				cancer=cancer,
				outputDir=outputDir,
				rmdupBam=rmdup.rmdup[1],
				codes_dir=codes_dir,
				project=project,
				purity=tumor_content.purity
	}
	call dealwithsnvindel{
	input:
		codes_dir=codes_dir,
		project=project,
		outputDir=outputDir,
		tumor=tumor,
		cancer=cancer,
		anno=annovar.anno
	}
	call MMR{
		input:
			codes_dir=codes_dir,
			tumor=tumor,
			outputDir=outputDir,
			snv=dealwithsnvindel.snv
	}
	call HRR{
		input:
			codes_dir=codes_dir,
			tumor=tumor,
			outputDir=outputDir,
			snv=dealwithsnvindel.snv
	}
	call HLA{
		input:
			inputDir=inputDir,
			outputDir=outputDir,
			normal=normal,
			newdir=create_dir.newdir
	}
	call neoantigen{
		input:
			codes_dir=codes_dir,
			outputDir=outputDir,
			normal=normal,
			tumor=tumor,
			hla=HLA.hla,
			vcf=mutation_calling.vcf
	}
	call MSI{
		input:
			bed=bed,
			codes_dir=codes_dir,
            tumor=tumor,
            outputDir=outputDir,
            rmdupBam=rmdup.rmdup[1]
    }
	call hereditary{
		input:		
			codes_dir=codes_dir,
			tumor=tumor,
			outputDir=outputDir,
			project=project,
			snv=dealwithsnvindel.snv
	}
	call auto_report{
		input:
			outputDir=outputDir,
			tumor=tumor,
			normal=normal,
			cancer=cancer,
			codes_dir=codes_dir,
			qc_2=qc_2.qc,
			concordance=conpair.concordance,
			snv_result=dealwithsnvindel.snv,
			cnv_result=cnvkit.cnv,
			fusion_result=fusion.fusion,
			tmb=TMB.tmb
	}
}


#create project directory
task create_dir{
    String outputDir
    command <<<
        #创建目录
        if [ ! -d ${outputDir} ];then
            mkdir ${outputDir}
        fi

        #创建qc目录
        if [ ! -d ${outputDir}/qc ];then
            mkdir ${outputDir}/qc
        fi

        #创建alignment目录
        if [ ! -d ${outputDir}/alignment ];then
            mkdir ${outputDir}/alignment
        fi

        #创建mutation目录
        if [ ! -d ${outputDir}/mutation ];then
            mkdir ${outputDir}/mutation
        fi

        #创建cnv目录
        if [ ! -d ${outputDir}/cnvkit ];then
           mkdir ${outputDir}/cnvkit
        fi
		
		#创建chemo目录
        if [ ! -d ${outputDir}/chemo ];then
            mkdir ${outputDir}/chemo
        fi

        #创建fusion目录
        if [ ! -d ${outputDir}/fusion ];then
            mkdir ${outputDir}/fusion
        fi
		
		#创建MSI目录
		if [ ! -d ${outputDir}/MSI ];then
            mkdir ${outputDir}/MSI
        fi
		
		#创建MMR目录
		if [ ! -d ${outputDir}/MMR ];then
			mkdir ${outputDir}/MMR
		fi
		
		#创建HPD目录
        if [ ! -d ${outputDir}/HPD ];then
            mkdir ${outputDir}/HPD
        fi
		
		##创建HRR目录
		if [ ! -d ${outputDir}/HRR ];then
			mkdir ${outputDir}/HRR
		fi
		
		#创建neoantigen目录
        if [ ! -d ${outputDir}/neoantigen/HLA ];then
            mkdir -p ${outputDir}/neoantigen/HLA
        fi
		
		#创建hereditary目录
        if [ ! -d ${outputDir}/hereditary ];then
            mkdir ${outputDir}/hereditary
        fi
		
		#创建report目录
        if [ ! -d ${outputDir}/report ];then
            mkdir -p ${outputDir}/report
        fi
		
    >>>
	output{
		String newdir = "${outputDir}/report"
      }
}

#generator raw fastq to clean fastq
task changehead{
	String newdir
    String tumor
    String inputDir
    String outputDir
	String read
	
	command <<<
		seqkit replace -p "/${read}" -r " ${read}" -j 10 ${inputDir}/*_${tumor}_*${read}.fq.gz -o ${outputDir}/qc/${tumor}_changehead_R${read}.fq
	>>>
	
	output{
		String outputFile = "${outputDir}/qc/${tumor}_changehead_R${read}.fq"
	}
	
}
task qc_normal{
	Array[String] data
	String normal
	String inputDir
	String outputDir

    command <<<
        echo processing raw reads with fastp
        fastp -i ${inputDir}/*_${normal}_*1.fq.gz -o ${outputDir}/qc/${normal}_clean_R1.fq.gz \
        -I ${inputDir}/*_${normal}_*2.fq.gz -O ${outputDir}/qc/${normal}_clean_R2.fq.gz \
        -w 10 \
		--correction \
        --overlap_len_require 20 \
        --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
        --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
        -j ${outputDir}/qc/${normal}.json \
        -h ${outputDir}/qc/${normal}.html --report_title ${normal} -e 20
	
    >>>

    output{
        Array[String] outputFile = [
        "${outputDir}/qc/${normal}_clean_R1.fq.gz",
        "${outputDir}/qc/${normal}_clean_R2.fq.gz",
        "${outputDir}/qc/${normal}.json",
        "${outputDir}/qc/${normal}.html"
        ]
    }
}
task qc{
    String tumor
    String inputDir
    String outputDir
    String codes_dir
    Array[String] data

    command <<<
        echo processing raw reads with fastp
        fastp -i ${outputDir}/qc/${tumor}_changehead_R1.fq -o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
        -I ${outputDir}/qc/${tumor}_changehead_R2.fq -O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
        -w 10 \
		-U --umi_loc=per_read --umi_len=4 --umi_prefix=UMI --umi_skip=3 \
	    --disable_trim_poly_g \
       	--disable_quality_filtering \
        --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
        --adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
		--correction \
		--overlap_len_require 10 \
        -j ${outputDir}/qc/${tumor}.json \
        -h ${outputDir}/qc/${tumor}.html --report_title ${tumor}

		# UMI
		python3 ${codes_dir}/UMI_Project.py -i ${inputDir} -o ${outputDir} -t ${tumor}
	
	rm ${outputDir}/qc/${tumor}_changehead_R1.fq ${outputDir}/qc/${tumor}_changehead_R2.fq
    >>>

    output{
        Array[String] outputFile = [
        "${outputDir}/qc/${tumor}_clean_R1.fq.gz",
        "${outputDir}/qc/${tumor}_clean_R2.fq.gz",
        "${outputDir}/qc/${tumor}.json",
        "${outputDir}/qc/${tumor}.html"
        ]
    }
}
#alignment clean fastq to reference
task alignment_bwa{
      String name
      String ref
      String outputDir
      Array[String] qc_T
      Array[String] qc_N
      command<<<

         bwa mem -R '@RG\tID:group_n\tLB:library_n\tPL:BGI\tPU:unit1\tSM:${name}' -M -t 10 ${ref} \
          ${outputDir}/qc/${name}_clean_R1.fq.gz ${outputDir}/qc/${name}_clean_R2.fq.gz | \
          samtools view -@ 5 -bh  -o - | samtools sort -@ 5  -o ${outputDir}/alignment/${name}.sorted.bam

          samtools index ${outputDir}/alignment/${name}.sorted.bam

      >>>

      output{
          String sorted = "${outputDir}/alignment/${name}.sorted.bam"
      }
}
##rmdup
task rmdup{
	String name
	String outputDir
	String ref
	String bam
	command<<<
		gencore -i ${outputDir}/alignment/${name}.sorted.bam -o ${outputDir}/alignment/${name}.rmdup.bam \
	    -r ${ref} -j ${outputDir}/qc/${name}_rmdup.json -h ${outputDir}/qc/${name}_rmdup.html

		samtools index ${outputDir}/alignment/${name}.rmdup.bam
	>>>
	output{
          String rmdup = "${outputDir}/alignment/${name}.rmdup.bam"
      }
}
# generater mpileup file
task generater_mpileup{
	String rmdup			
    String name
    String ref
    String bed
    String outputDir

    command<<<

		samtools mpileup -Bq 20 -Q 20  -f ${ref} -l ${bed} \
		${outputDir}/alignment/${name}.rmdup.bam -o ${outputDir}/alignment/${name}.pileup

    >>>

    output{
        String pileup = "${outputDir}/alignment/${name}.pileup"
    }
}
task mutation_calling{
	String tumor
	String rmdup
	String outputDir
	String ref
	String bed
	String codes_dir
	String normal
	command<<<
##1条call	
		java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar -G ${ref} \
        -f 0.002 -N ${tumor} -b ${outputDir}/alignment/${tumor}.rmdup.bam  \
        -UN -Q 20 -m 3 -r 3 -th 20 -c 1 -S 2 -E 3 -g 4 ${bed} | /dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${tumor} -E -f 0.002 >${outputDir}/mutation/${tumor}.1r.snp.indel.vcf
##提取2条矫正的序列和NM<4的序列
		python3 ${codes_dir}/fetch_bam.py ${outputDir} ${tumor}
##2条矫正的call		
		java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar -G ${ref} \
		-f 0.0001 -N ${tumor}_2r -b ${outputDir}/alignment/${tumor}.2r.rmdup.bam \
		-UN -Q 20 -m 3 -r 3 -th 20 -c 1 -S 2 -E 3 -g 4 ${bed} | /dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
		 | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${tumor} -E -f 0.001 >${outputDir}/mutation/${tumor}.2r.snp.indel.vcf

		##merge突变，以1条方式call的>0.01的突变+两条方式的对一条方式的低频区域（AF<0.01）进行矫正。
		perl ${codes_dir}/1r_plus_2r.pl ${outputDir} ${tumor}

		##去除control，control 5%以上的cfDNA都去除，1%-5%的，cfDNA/control<5 的都去除。
		perl ${codes_dir}/t_subs_n_vcf.pl ${outputDir} ${tumor} ${normal}

		##add msi and strandbias flag
		perl ${codes_dir}/add_flag.pl ${outputDir} ${tumor} ${normal}

		##add malt flag
		grep -v ^# ${outputDir}/mutation/${tumor}_substract_${normal}.snp.indel.vcf | awk '{OFS="\t"}{print $1,$2-1,$2}' - \
		>${outputDir}/mutation/${tumor}_substract_${normal}.snp.indel.bed

		samtools mpileup -aBq 20 -Q 20 -f ${ref} -l ${outputDir}/mutation/${tumor}_substract_${normal}.snp.indel.bed \
                ${outputDir}/alignment/${tumor}.2r.rmdup.bam -o ${outputDir}/alignment/${tumor}_substract_${normal}.snp.indel.pileup

		python ${codes_dir}/add_malt.py ${outputDir} ${tumor} ${normal}

		##filter flag
		perl ${codes_dir}/filter_flag.pl ${outputDir} ${tumor} ${normal}  
	>>>
	
	output{
		String vcf = "${outputDir}/mutation/${tumor}_substract_${normal}.filter.flag.snp.indel.vcf"        
	}
}
task mutation_calling_normal{
	String normal
	String rmdup
	String outputDir
	String ref
	String bed
	
	command<<<
	    java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar -G ${ref} \
        -f 0.01 -N ${normal} -b ${outputDir}/alignment/${normal}.rmdup.bam \
        -Q 20 -r 3 -th 20 -c 1 -S 2 -E 3 -g 4 ${bed} | /dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${normal} -E -f 0.01 >${outputDir}/mutation/${normal}.snp.indel.vcf
	>>>
	
	output{
		String vcf = "${outputDir}/mutation/${normal}.snp.indel.vcf"        
	}
}
# hotspot
task hotspot{
	String tumor
	String outputDir
	String ref
	String rmdupBam
	String codes_dir
	command<<<
	
	mkdir -p ${outputDir}/mutation/hotspot
	samtools mpileup -Bq 20 -Q 20  -f ${ref} -l /dataseq/jmdna/codes/public/hotspot.bed ${rmdupBam} -o ${outputDir}/mutation/hotspot/${tumor}.hotspot.pileup
	java -jar $VARSCAN mpileup2cns ${outputDir}/mutation/hotspot/${tumor}.hotspot.pileup --min-var-freq 0.001 --min-avg-qual 20 --output-vcf 1 --variants --p-value 0.99 --min-reads2 2 --strand-filter 0 >${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.vcf
#	java -jar $VARSCAN mpileup2cns ${outputDir}/mutation/hotspot/${tumor}.hotspot.pileup --min-var-freq 0.002 --min-avg-qual 20 --output-vcf 1 --variants --p-value 0.99 --min-reads2 3 --strand-filter 1 >${outputDir}/mutation/hotspot/${tumor}.hotspot.H.snp.indel.vcf
#	perl ${codes_dir}/hotspot.hvl.pl ${outputDir} ${tumor} 

#	if [ -e "${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.vcf" ]; then
		table_annovar.pl \
		${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.vcf \
		/dataseq/jmdna/software/annovar/humandb/ \
		-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
		-protocol refGene \
		-argument '-hgvs' \
		-operation g \
		--outfile ${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.anno

#	fi
	perl ${codes_dir}/hotspot.filter.pl ${outputDir} ${tumor}
	>>>
	output{
				String  hotspot = "${outputDir}/mutation/hotspot/${tumor}.hotspot.snp.indel.filter.anno.hg19_multianno.txt"
	}
}
task annovar{
	String codes_dir
	String tumor
	String normal
    String outputDir
    String tvcf
	String nvcf
    command<<<
		perl ${codes_dir}/t_subs_n_vcf.pl ${outputDir} ${tumor} ${normal}

        table_annovar.pl \
        ${outputDir}/mutation/${tumor}_substract_${normal}.filter.flag.snp.indel.vcf \
        /dataseq/jmdna/software/annovar/humandb/ \
        -buildver hg19 -nastring . -vcfinput -remove -otherinfo \
        -protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
	-argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
	--intronhgvs 50 \
        -operation g,f,f,f,f,f,f,f,f,f,r \
	--outfile ${outputDir}/mutation/${tumor}.snp.indel.Somatic.annoall

        table_annovar.pl \
        ${outputDir}/mutation/${normal}.snp.indel.vcf \
        /dataseq/jmdna/software/annovar/humandb/ \
        -buildver hg19 -nastring . -vcfinput -remove -otherinfo \
	-protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
        -argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
	--intronhgvs 50 \
	-operation g,f,f,f,f,f,f,f,f,f,r \
	--outfile ${outputDir}/mutation/${tumor}.snp.indel.Germline.anno

    >>>
	output{
        Array[String] anno = [
        "${outputDir}/mutation/${tumor}.snp.indel.Germline.anno.hg19_multianno.txt",
        "${outputDir}/mutation/${tumor}.snp.indel.Somatic.annoall.hg19_multianno.txt",
        ]
    }
}
task qc_2{
	String ref
	String bed
	String name
	String tumor
	String outputDir
	String codes_dir
	#for task chain
	Array[String] anno 
	
	command <<<

		samtools flagstat -@ 10 ${outputDir}/alignment/${name}.rmdup.bam >${outputDir}/qc/${name}.rmdup.flagstat
		samtools stats --reference ${ref} -t ${bed} -@ 10 ${outputDir}/alignment/${name}.rmdup.bam > ${outputDir}/alignment/${name}.stat
		mkdir ${outputDir}/qc/${name}_sorted_bamdst ${outputDir}/qc/${name}_rmdup_bamdst
        bamdst -p ${bed} -o ${outputDir}/qc/${name}_sorted_bamdst ${outputDir}/alignment/${name}.sorted.bam
		bamdst -p ${bed} -o ${outputDir}/qc/${name}_rmdup_bamdst ${outputDir}/alignment/${name}.rmdup.bam			
		Rscript ${codes_dir}/InsertAndDepthStat.R ${outputDir}/qc/${name}_InsertAndDepthStat ${outputDir}/qc/${name}_rmdup_bamdst/insertsize.plot ${outputDir}/qc/${name}_rmdup_bamdst/depth_distribution.plot

		python3 ${codes_dir}/qc_stat_umi.py ${outputDir} ${name} ${tumor}

	>>>
	output{
		String qc = "${outputDir}/qc/${name}_qc.txt"
	}
}
task fusion{
	String ref
	String codes_dir
	String tumor
	String cancer
	String outputDir
	#for task chain
	String Bam
	String project

	command<<<
		java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -Xmx12G  -jar $PICARD MarkDuplicates \
        I=${outputDir}/alignment/${tumor}.sorted.bam \
        O=${outputDir}/alignment/${tumor}.picard.rmdup.bam  \
        CREATE_INDEX=true \
        M=${outputDir}/alignment/${tumor}.picard.rmdup.metrics.txt  \
        R=${ref}
		
		# Extract the discordant paired-end alignments.
		samtools view -b -F 1294 ${outputDir}/alignment/${tumor}.picard.rmdup.bam > ${outputDir}/fusion/${tumor}.discordants.bam

		# Extract the split-read alignments
		samtools view -h ${outputDir}/alignment/${tumor}.picard.rmdup.bam \
		| /dataseq/jmdna/software/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin \
		| samtools view -Sb - \
		> ${outputDir}/fusion/${tumor}.splitters.bam

		lumpyexpress \
		-B ${outputDir}/alignment/${tumor}.picard.rmdup.bam \
		-S ${outputDir}/fusion/${tumor}.splitters.bam \
		-D ${outputDir}/fusion/${tumor}.discordants.bam \
		-o ${outputDir}/fusion/${tumor}.fusion.vcf

		perl ${codes_dir}/fusion.filter.pl ${outputDir}/fusion/${tumor}.fusion.vcf ${outputDir}/fusion/${tumor}.fusion.filter.vcf

		svtyper \
		-B ${outputDir}/alignment/${tumor}.picard.rmdup.bam \
		-i ${outputDir}/fusion/${tumor}.fusion.filter.vcf \
		-T ${ref} \
		-o ${outputDir}/fusion/${tumor}.fusion.gt.vcf

		table_annovar.pl \
		${outputDir}/fusion/${tumor}.fusion.gt.vcf \
		/dataseq/jmdna/software/annovar/humandb/ \
		-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
		-protocol refGene \
		-operation g \
		--outfile ${outputDir}/fusion/${tumor}.fusion
	
		perl ${codes_dir}/fusion.reanno.624.pl ${outputDir}/qc/${tumor}_sorted_bamdst/depth.tsv.gz ${outputDir} ${tumor}
		perl ${codes_dir}/fusion_targetTherapy.pl ${codes_dir} ${tumor} ${outputDir} ${project} ${cancer}

	>>>
	
	output{
        String fusion = "${outputDir}/fusion/${tumor}.fusion.pos.txt"
    }
}
task TMB{
	String codes_dir
	String tumor
	String outputDir
	Array[String] anno
	
	command <<<	
		perl ${codes_dir}/tmb_umi.pl ${outputDir} ${tumor}
		python3 ${codes_dir}/correct_f1r1_tmb.py ${outputDir} ${tumor}
	>>>
	output{
		String tmb="${outputDir}/mutation/${tumor}.tmb.txt"
	}
}

task conpair{
	String tumor
	String normal
	String outputDir
	String ref
	#for task chain
	Array[String] rmdupBam
	command <<<

		python3 /dataseq/jmdna/software/Conpair-master/scripts/run_gatk_pileup_for_sample.py \
		-M /dataseq/jmdna/software/Conpair-master/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed \
		-B ${outputDir}/alignment/${normal}.rmdup.bam \
		-O ${outputDir}/alignment/${normal}.gatk.mpileup \
		-R ${ref} \
		-G /dataseq/jmdna/software/GenomeAnalysisTK.3.7.jar
		
		python3 /dataseq/jmdna/software/Conpair-master/scripts/run_gatk_pileup_for_sample.py \
		-M /dataseq/jmdna/software/Conpair-master/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed \
		-B ${outputDir}/alignment/${tumor}.rmdup.bam \
		-O ${outputDir}/alignment/${tumor}.gatk.mpileup \
		-R ${ref} \
		-G /dataseq/jmdna/software/GenomeAnalysisTK.3.7.jar
	
		sed -i 's/^chr//g' ${outputDir}/alignment/${normal}.gatk.mpileup
		sed -i 's/^chr//g' ${outputDir}/alignment/${tumor}.gatk.mpileup

			
		python3 /dataseq/jmdna/software/Conpair-master/scripts/verify_concordance.py \
		-T ${outputDir}/alignment/${tumor}.gatk.mpileup \
		-N ${outputDir}/alignment/${normal}.gatk.mpileup \
		-H \
		-O ${outputDir}/qc/${tumor}_concordance.txt
		
		python3 /dataseq/jmdna/software/Conpair-master/scripts/estimate_tumor_normal_contamination.py \
		-T ${outputDir}/alignment/${tumor}.gatk.mpileup \
		-N ${outputDir}/alignment/${normal}.gatk.mpileup \
		-O ${outputDir}/qc/${tumor}_contamination.txt				

	>>>
	output{
		Array[String] concordance = [
        "${outputDir}/report/qc/${tumor}_concordance.txt",
		"${outputDir}/report/qc/${tumor}_contamination.txt",
		]
	}
}

task chemoTherapy{
		String codes_dir
		String normal
		String outputDir
		String ref
		String project
		String rmdupBam
		command <<<
			${codes_dir}/chemo/chemo_panel.py -p ${project} -o ${outputDir} --n ${normal} --r ${ref}
        >>>
}

task tumor_content{
	String ref
	String tumor
	String normal
	String outputDir
	String gc_wiggle
	String codes_dir
	#for task chain
	Array[String] pileup
	
	command <<<

		sequenza-utils bam2seqz -p -gc ${gc_wiggle} \
		-F ${ref} \
		-n ${outputDir}/alignment/${normal}.pileup \
		-t ${outputDir}/alignment/${tumor}.pileup | gzip >${outputDir}/qc/target_${tumor}.200base.seqz.gz
		sequenza-utils seqz_binning -w 200 -s ${outputDir}/qc/target_${tumor}.200base.seqz.gz | gzip  > ${outputDir}/qc/target_${tumor}.200base.small.seqz.gz

        Rscript ${codes_dir}/sequenza.R ${tumor} ${outputDir}/qc/target_${tumor}.200base.small.seqz.gz ${outputDir}/qc/sequenza || echo "sequenza failed!"
		
	>>>
	output{
        String purity = "${outputDir}/qc/sequenza/${tumor}_CP_contours.pdf"
    }
}

task cnvkit{
    String tumor
    String outputDir
    String cancer
    String codes_dir
    String project
    #for task chain
    String rmdupBam
	String purity

    command <<<

	echo run cnvkit batch to processing cnv calling
	cnvkit.py batch \
	${rmdupBam} \
	-r ${codes_dir}/cnvkit/624gene_pool_normal_reference.cnn \
	--drop-low-coverage  --scatter --diagram --output-dir ${outputDir}/cnvkit

	cnvkit.py scatter \
	${outputDir}/cnvkit/${tumor}.rmdup.cnr -s ${outputDir}/cnvkit/${tumor}.rmdup.cns \
	--y-max 3 --y-min -3 \
	--title ${tumor}.cns \
	-o ${outputDir}/cnvkit/${tumor}.cnv.png

    if [ -e "${outputDir}/qc/sequenza/${tumor}_confints_CP.txt" ]; then
        # absolute copy number
        cnvkit.py call \
        -m clonal \
        ${outputDir}/cnvkit/${tumor}.rmdup.cns \
        -y \
        --purity `head -n2 ${outputDir}/qc/sequenza/${tumor}_confints_CP.txt |tail -n1|cut -f1` \
        --drop-low-coverage  \
        --filter ampdel \
        -o ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn.hc
    fi        
	perl ${codes_dir}/log2_cn.pl ${outputDir}/cnvkit/${tumor}.rmdup.cns ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn	
	perl ${codes_dir}/cnv_targetTherapy.pl ${codes_dir} ${tumor} ${outputDir} ${project} ${cancer}
    >>>

	output{
        String cnv = "${outputDir}/cnvkit/${tumor}.rmdup.cns"
    	}
}

task dealwithsnvindel{
	String codes_dir
	String project
	String outputDir
	String tumor
	Array[String] anno
	String cancer

	command <<<
	
	perl ${codes_dir}/pick_variant_control_umi.pl ${outputDir} ${tumor}
	python3 ${codes_dir}/correct_f1r1.py ${outputDir} ${tumor}
	perl ${codes_dir}/pick_mut_splice_promoter_control.pl ${codes_dir} ${tumor} ${outputDir} ${project}
	perl ${codes_dir}/germline_targetTherapy.pl ${tumor} ${outputDir} ${project} ${cancer}
	perl ${codes_dir}/targetTherapy.pl ${tumor} ${outputDir} ${project} ${cancer}
	
	>>>
    output{
        String snv = "${outputDir}/mutation/${tumor}.snvindel.pos.txt"
    }
}

task MMR{
	String codes_dir
	String tumor
	String outputDir
	String snv
	command <<<
			perl ${codes_dir}/mmr_controlsample.pl ${outputDir} ${tumor}
	>>>
	output{
			String mmr_out = "${outputDir}/MMR/${tumor}_mmr.txt"
		}
}

task HRR{
	String codes_dir
	String tumor
	String outputDir
	String snv
	command <<<
			perl ${codes_dir}/hrr_controlsample_cfDNA.pl ${outputDir} ${tumor}
	>>>
	output{
			String mmr_out = "${outputDir}/HRR/${tumor}_hrr.txt"
		}
}

task HLA{
	String inputDir
	String outputDir
	String normal
	String newdir
	command <<<

		razers3 -tc 10 -i 95 -m 1 -dr 0 -o ${outputDir}/neoantigen/HLA/fished_1.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta ${inputDir}/*_${normal}_*1.fq.gz
		samtools bam2fq ${outputDir}/neoantigen/HLA/fished_1.bam > ${outputDir}/neoantigen/HLA/${normal}_1_fished.fastq
		rm ${outputDir}/neoantigen/HLA/fished_1.bam 
		razers3 -tc 10 -i 95 -m 1 -dr 0 -o ${outputDir}/neoantigen/HLA/fished_2.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta ${inputDir}/*_${normal}_*2.fq.gz
		samtools bam2fq ${outputDir}/neoantigen/HLA/fished_2.bam > ${outputDir}/neoantigen/HLA/${normal}_2_fished.fastq
		rm ${outputDir}/neoantigen/HLA/fished_2.bam
		/dataseq/jmdna/software/OptiType-1.3.5/OptiTypePipeline.py -i ${outputDir}/neoantigen/HLA/${normal}_1_fished.fastq  ${outputDir}/neoantigen/HLA/${normal}_2_fished.fastq --dna -v --prefix ${normal} -o ${outputDir}/neoantigen/HLA/

	>>>
	output{
        String hla = "${outputDir}/neoantigen/HLA/${normal}_result.tsv"
    }
}
task neoantigen{
	String codes_dir
	String outputDir
	String normal
	String tumor
	String hla
	String vcf 
	command <<<
		sh ${codes_dir}/predict_neoantigen.sh ${outputDir} ${normal} ${tumor} ${codes_dir}
	>>>
	output{
        String neoantigen = "${outputDir}/neoantigen/MHC_Class_I/${tumor}.all_epitopes.netchop.txt"
    }
}

task MSI{
    String bed
	String codes_dir
    String tumor
    String outputDir
    String rmdupBam

    command <<<
		##msings
		echo ${outputDir}/alignment/${tumor}.rmdup.bam >${outputDir}/MSI/bam.list
		${codes_dir}/MSI/run_msings.sh ${outputDir}/MSI/bam.list
		mv ${outputDir}/alignment/${tumor}.rmdup ${outputDir}/MSI/
		mv ${outputDir}/alignment/msi_run_log.txt ${outputDir}/MSI/
		mv ${outputDir}/alignment/Combined_MSI.txt ${outputDir}/MSI/
		##msisensor2
        msisensor2 msi -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 -t ${rmdupBam} -e ${bed} -b 10 -o ${outputDir}/MSI/${tumor}.msi
    >>>
    output{
        String target="${outputDir}/MSI/${tumor}.msi"
    }
}

task hereditary{
		String codes_dir
		String tumor
		String outputDir
		String project
		String snv
		command <<<
			python3 /dataseq/jmdna/codes/624/hereditary/hereditary.py -p ${project} -o ${outputDir} --n ${tumor}
        >>>
}

task auto_report{
	String tumor
	String normal
	String cancer
	String outputDir
	String codes_dir
	Array[String] qc_2
	Array[String] concordance
	String snv_result
	String cnv_result
	String fusion_result	
	String tmb
	

	command <<<
		perl ${codes_dir}/hpd_control_umi.pl ${outputDir} ${tumor}
		python3 ${codes_dir}/sample_post.py -s ${tumor} -o ${outputDir} --n ${normal}
		perl ${codes_dir}/indication.pl ${outputDir} ${cancer}
		python3 ${codes_dir}/qc_check_control_cfdna.py ${outputDir} ${tumor} ${normal}
		python3 ${codes_dir}/drug_dedup.py ${outputDir} ${tumor}
		python3 ${codes_dir}/report_template/624gene_cfdna_control_report.py ${outputDir} ${tumor} ${normal} ${cancer}
		python3 ${codes_dir}/wdl_check.py -o ${outputDir}

		perl ${codes_dir}/file_format_change.pl ${outputDir} ${tumor}		
		cp ${outputDir}/qc/qc_fail.txt ${outputDir}/report/qc_fail.txt
		cp ${outputDir}/qc/${tumor}_qc.txt ${outputDir}/report/
		cp ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn ${outputDir}/report/
		cp ${outputDir}/cnvkit/${tumor}.cnv.png ${outputDir}/report/
		cp ${outputDir}/fusion/${tumor}.fuison.vus.txt ${outputDir}/report/
		cp ${outputDir}/fusion/${tumor}.fusion.reanno.vcf ${outputDir}/report/
#		cp ${outputDir}/mutation/*filter* ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.snvindel.Germline.target.txt ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.nontarget.vus.txt ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.snvindel.vus.txt ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.target.splicing.txt ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.target.promoter.txt ${outputDir}/report/
		cp ${outputDir}/mutation/${tumor}.tmb.txt ${outputDir}/report/
		cp ${outputDir}/MMR/${tumor}.mmr.pre.txt ${outputDir}/report/  
		cp ${outputDir}/HRR/${tumor}.hrr.pre.txt ${outputDir}/report/
		cp ${outputDir}/HPD/${tumor}.hpd.pre.txt ${outputDir}/report/
		cp ${outputDir}/hereditary/${tumor}.hereditary.pre.txt ${outputDir}/report/
		python3 ${codes_dir}/txt_xlsx.py ${outputDir} ${tumor}
	>>>
}