#@UGENE_WORKFLOW
#Reading
#convert SAM to BAM, sort BAM,
#VariantCalling with Samtools



workflow SamTools_JT{

    call_variants {
        type:call_variants;
        name:"Поиск вариабельных позиций с помощью SAMtools";
        capq_thres:50;
        indel_frac:1;
        max_depth:1000000;
        max_indel_depth:100000;
        min-end-distance:0;
        min_baseq:30;
        pref:0.999;
        ptype:"";
        reference-source:port;
        theta:0.01;
        variants-url:s1-3.vcf;
    }
    files-conversion {
        type:files-conversion;
        name:"Преобразование форматов файлов";
        document-format:bam;
    }
    Sort-bam {
        type:Sort-bam;
        name:"Сортировка BAM-файлов";
    }
    read-sequence-2 {
        type:read-sequence;
        name:"Чтение последовательности 2";
        url-in {
            dataset:"Dataset 1";
            file:"D:/Томилова/sample/hbv+AdV.fasta";
        }
    }
    get-file-list-1 {
        type:get-file-list;
        name:"Получение списка файлов 1";
        url-in {
            dataset:"Dataset 1";
            file:"D:/UGENE/2022.02.09_16-12 S1-3/report/bwa/sS1-3.sam";
        }
    }

    .actor-bindings {
        files-conversion.out-file->Sort-bam.in-file
        get-file-list-1.out-url->files-conversion.in-file
        Sort-bam.out-file->call_variants.in-assembly
        read-sequence-2.out-sequence->call_variants.in-sequence
    }

    Sort-bam.url->call_variants.in-assembly.url
    read-sequence-2.url->call_variants.in-sequence.url
    get-file-list-1.url->files-conversion.in-file.url
    files-conversion.url->Sort-bam.in-file.url

    .meta {
        visual {
            Sort-bam {
                pos:"210 -180";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-file.angle:180;
                out-file.angle:360;
            }
            call_variants {
                pos:"315 0";
                style:ext;
                bg-color-ext:"0 128 128 64";
                bounds:"-30 -30 153 105";
                in-assembly.angle:150;
                in-sequence.angle:210;
                out-variations.angle:360;
            }
            files-conversion {
                pos:"225 -345";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-file.angle:180;
                out-file.angle:360;
            }
            get-file-list-1 {
                pos:"-120 -150";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-url.angle:360;
            }
            read-sequence-2 {
                pos:"60 -30";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            Sort-bam.out-file->call_variants.in-assembly {
                text-pos:"-50.5 -37";
            }
            files-conversion.out-file->Sort-bam.in-file {
                text-pos:"-17 -24";
            }
            get-file-list-1.out-url->files-conversion.in-file {
                text-pos:"-43 -24";
            }
            read-sequence-2.out-sequence->call_variants.in-sequence {
                text-pos:"-58 -24";
            }
        }
    }
}