task mutation_calling_umi {
    String name
    String output_dir
    String rmdup_bam
    String ref
    String bed
    command <<<

        if [ ! -d ${output_dir}/mutation ];then
        mkdir ${output_dir}/mutation
        fi


        #1条call
        # 这个情况是reads数目只有1，但是如果去掉了这个reads数导致数据量减少很多
        # -r 3 是指有3条这样样的reads支撑
        # -f 是指频率 以2条方式的call出来的变异频率可以比1条的方式更可信

        java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar \
        -G ${ref} \
        -f 0.001 \
        -N ${name} \
        -b ${rmdup_bam} \
        -UN -Q 20 -m 3 -r 3 -th 10 -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 ${name} -E -f 0.001 > ${output_dir}/mutation/${name}.1r.snp.indel.vcf

        #提取>=2条矫正的序列
        python3 /home/zhangchao/project/pipeline/control/script/fetch_bam.py ${output_dir}/alignment/${name}.rmdup.bam ${output_dir}/alignment/${name}.2r.rmdup.bam
        samtools index ${output_dir}/alignment/${name}.2r.rmdup.bam

        # 保证 1r call mut umi family 里面有2条reads
        #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 ${name}_2r -b ${output_dir}/alignment/${name}.2r.rmdup.bam \
        -UN -Q 20 -m 3 -r 1 -th 10 -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 ${name} -E -f 0.001 >${output_dir}/mutation/${name}.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  /home/zhangchao/project/pipeline/control/script/1r_plus_2r.pl \
        ${output_dir}/mutation/${name}.1r.snp.indel.vcf \
        ${output_dir}/mutation/${name}.2r.snp.indel.vcf \
        ${output_dir}/mutation/${name}.snp.indel.vcf

        table_annovar.pl \
        ${output_dir}/mutation/${name}.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 ${output_dir}/mutation/${name}.snp.indel.anno

    >>>

    output {
        String vcf = "${output_dir}/mutation/${name}.filter.flag.snp.indel.vcf"
    }
}

task mutation_calling_tissue {
    String name
    String bed
    String ref
    String output_dir
    String rmdup_bam

    command <<<
        if [ ! -d ${output_dir}/mutation ];then
        mkdir ${output_dir}/mutation
        fi

        # vardict
        java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar \
        -G ${ref} \
        -f 0.01 \
        -N ${name} \
        -b ${rmdup_bam} \
        -UN \
        -Q 20 \
        -m 3 \
        -r 3 \
        -th 10 \
        -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 ${name} -E -f 0.01 >${output_dir}/mutation/${name}.snp.indel.vcf

        table_annovar.pl \
        ${output_dir}/mutation/${name}.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 \
        -argument '-splicing_threshold 2 -hgvs',,,,,,,,, \
        -operation g,f,f,f,f,f,f,f,f,f \
        --intronhgvs 50 \
        --outfile ${output_dir}/mutation/${name}.snp.indel.anno

    >>>

    output {
        String vcf = "${output_dir}/mutation/${name}.snp.indel.vcf"
    }
}

task mutation_calling_tissue_control {
    String name
    String bed
    String ref
    String output_dir
    String tumor_rmdup_bam
    String normal_rmdup_bam

    command <<<
        if [ ! -d ${output_dir}/mutation ];then
        mkdir ${output_dir}/mutation
        fi

        java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar \
        -G ${ref} \
        -f 0.01 \
        -N ${name} \
        -b "${tumor_rmdup_bam}|${normal_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/testsomatic.R \
        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_paired.pl -N ${name} -f 0.01 > ${output_dir}/mutation/${name}.snp.indel.vcf

        table_annovar.pl \
        ${output_dir}/mutation/${name}.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 \
        -argument '-splicing_threshold 2 -hgvs',,,,,,,,, \
        -operation g,f,f,f,f,f,f,f,f,f \
        --intronhgvs 50 \
        --outfile ${output_dir}/mutation/${name}.snp.indel.anno

    >>>

    output {
        String vcf = "${output_dir}/mutation/${name}.snp.indel.vcf"
    }
}

workflow call_mutation {

    String tumor
    String tumor_rmdup_bam
    String? normal
    String? normal_rmdup_bam
    Boolean umi
    String output_dir
    String ref
    String bed

    scatter(name in [tumor, normal]) {
        if (defined(name)) {
            if (name==tumor) {
                if (umi) {
                    call mutation_calling_umi as tumor_mutation_calling_umi {
                        input:
                            name=name,
                            output_dir=output_dir,
                            ref=ref,
                            bed=bed,
                            rmdup_bam=tumor_rmdup_bam
                    }
                }
                if (!umi) {
                    # 单样本模式，normal没有定义
                    if (name==select_first([normal, tumor])) {
                        call mutation_calling_tissue as tumor_mutation_calling_tissue {
                            input:
                                name=name,
                                output_dir=output_dir,
                                ref=ref,
                                bed=bed,
                                rmdup_bam=normal_rmdup_bam
                        }
                    }
                    # 双样本模式，normal有定义
                    if (name!=select_first([normal, tumor])) {
                        call mutation_calling_tissue_control as tumor_mutation_calling_tissue_control {
                            input:
                                name=name,
                                output_dir=output_dir,
                                ref=ref,
                                bed=bed,
                                tumor_rmdup_bam=tumor_rmdup_bam,
                                normal_rmdup_bam=normal_rmdup_bam
                        }
                    }
                }
            }
            if (name==select_first([normal, 'None'])) {
                if (umi) {
                    call mutation_calling_tissue as normal_mutation_calling_tissue {
                        input:
                            name=name,
                            output_dir=output_dir,
                            ref=ref,
                            bed=bed,
                            rmdup_bam=normal_rmdup_bam
                    }
                }

            }

        }
    }

    output {
        String somatic_vcf = "${output_dir}/mutation/${tumor}.snp.indel.vcf"
        String somatic_nc_vcf = "${output_dir}/mutation/${normal}.snp.indel.vcf"
    }
}