#@UGENE_WORKFLOW
#The workflow takes FASTQ files as input and process this data as follows:
#    - Filters the input sequencing reads by the CASAVA header (for Illumina platform).
#    - Cuts of adapter sequences.
#    - Trims the sequencing reads by quality.
#    - Merges different FASTQ files.
#    - Maps the sequencing reads by TopHat.
#
#The workflow also performs quality control of the data with FastQC: first, on the input FASTQ files and, second, after the pre-processing step.
#
#Besides intermediate files and FastQC reports, the final result is a BAM file with aligned reads and other TopHat output files.
#



workflow "Processing of raw RNA-Seq paired-end reads with mapping"{

    CASAVAFilter {
        type:CASAVAFilter;
        name:"Filter Reads by CASAVA Header";
        custom-dir:filtered_fastq;
    }
    QualityTrim {
        type:QualityTrim;
        name:"Trim Reads by Quality";
        custom-dir:filtered_fastq;
        len-id:10;
        out-mode:0;
        qual-id:20;
    }
    get-file-list {
        type:get-file-list;
        name:"Read FASTQ Files with Reads 1";
        url-in {
            dataset:"Dataset 1";
        }
    }
    MergeFastq {
        type:MergeFastq;
        name:"Merge FASTQ Files";
        custom-dir:filtered_fastq;
        out-mode:0;
        out-name:in_1.fq;
    }
    tophat {
        type:tophat;
        name:"Map RNA-Seq Reads with TopHat";
        bowtie-version:1;
        mate-inner-distance:170;
        no-novel-junctions:true;
        out-dir:output;
    }
    get-file-list-1 {
        type:get-file-list;
        name:"Read FASTQ Files with Reads 2";
        url-in {
            dataset:"Dataset 1";
        }
    }
    CASAVAFilter-1 {
        type:CASAVAFilter;
        name:"Filter Reads by CASAVA Header";
        custom-dir:filtered_fastq;
    }
    QualityTrim-1 {
        type:QualityTrim;
        name:"Trim Reads by Quality";
        custom-dir:filtered_fastq;
        len-id:10;
        out-mode:0;
        qual-id:20;
    }
    MergeFastq-1 {
        type:MergeFastq;
        name:"Merge FASTQ Files";
        custom-dir:filtered_fastq;
        out-mode:0;
        out-name:in_2.fq;
    }
    multiplexer {
        type:multiplexer;
        name:Multiplexer;
    }
    CutAdaptFastq {
        type:CutAdaptFastq;
        name:"Cut Adapter";
        out-mode:0;
    }
    CutAdaptFastq-1 {
        type:CutAdaptFastq;
        name:"Cut Adapter";
        out-mode:0;
    }
    fastqc {
        type:fastqc;
        name:"FastQC Quality Control";
    }
    fastqc-1 {
        type:fastqc;
        name:"FastQC Quality Control";
    }
    fastqc-2 {
        type:fastqc;
        name:"FastQC Quality Control";
    }
    fastqc-3 {
        type:fastqc;
        name:"FastQC Quality Control";
    }
    fastqc-2-1 {
        type:fastqc;
        name:"FastQC Quality Control";
    }

    .actor-bindings {
        get-file-list-1.out-url->CASAVAFilter-1.in-file
        get-file-list-1.out-url->fastqc.in-file
        QualityTrim.out-file->MergeFastq.in-file
        get-file-list.out-url->CASAVAFilter.in-file
        get-file-list.out-url->fastqc-1.in-file
        MergeFastq.out-file->multiplexer.input-data-1
        MergeFastq.out-file->fastqc-3.in-file
        tophat.out-assembly->fastqc-2-1.in-file
        CASAVAFilter-1.out-file->CutAdaptFastq.in-file
        QualityTrim-1.out-file->MergeFastq-1.in-file
        MergeFastq-1.out-file->multiplexer.input-data-2
        MergeFastq-1.out-file->fastqc-2.in-file
        multiplexer.output-data->tophat.in-sequence
        CutAdaptFastq.out-file->QualityTrim-1.in-file
        CutAdaptFastq-1.out-file->QualityTrim.in-file
        CASAVAFilter.out-file->CutAdaptFastq-1.in-file
    }

    get-file-list.url->CASAVAFilter.in-file.url
    CutAdaptFastq-1.url->QualityTrim.in-file.url
    QualityTrim.url->MergeFastq.in-file.url
    MergeFastq.url->tophat.in-sequence.in-url
    MergeFastq-1.url->tophat.in-sequence.paired-url
    get-file-list-1.url->CASAVAFilter-1.in-file.url
    CutAdaptFastq.url->QualityTrim-1.in-file.url
    QualityTrim-1.url->MergeFastq-1.in-file.url
    CASAVAFilter-1.url->CutAdaptFastq.in-file.url
    CASAVAFilter.url->CutAdaptFastq-1.in-file.url
    get-file-list-1.url->fastqc.in-file.url
    get-file-list.url->fastqc-1.in-file.url
    MergeFastq-1.url->fastqc-2.in-file.url
    MergeFastq.url->fastqc-3.in-file.url
    tophat.hits-url->fastqc-2-1.in-file.url

    .meta {
        parameter-aliases {
            CASAVAFilter.custom-dir {
                alias:casava1_out_dir;
            }
            CASAVAFilter.out-mode {
                alias:casava1_out_dir_type;
            }
            QualityTrim.custom-dir {
                alias:trim_reads2_out_dir;
            }
            QualityTrim.out-mode {
                alias:trim_reads2_out_dir_type;
            }
            get-file-list.url-in {
                alias:in;
            }
            tophat.bowtie-index-basename {
                alias:idx_name;
            }
            tophat.bowtie-index-dir {
                alias:idx_dir;
            }
            tophat.out-dir {
                alias:out_dir;
            }
            get-file-list-1.url-in {
                alias:in_mate;
            }
            CASAVAFilter-1.custom-dir {
                alias:casava2_out_dir;
            }
            CASAVAFilter-1.out-mode {
                alias:casava2_out_dir_type;
            }
            QualityTrim-1.custom-dir {
                alias:trim_reads1_out_dir;
            }
            QualityTrim-1.out-mode {
                alias:trim_reads1_out_dir_type;
            }
            fastqc.custom-dir {
                alias:fasqc1_out_dir;
            }
            fastqc.out-mode {
                alias:fasqc1_out_dir_type;
            }
            fastqc-1.custom-dir {
                alias:fasqc2_out_dir;
            }
            fastqc-1.out-mode {
                alias:fasqc2_out_dir_type;
            }
            fastqc-2.custom-dir {
                alias:fasqc3_out_dir;
            }
            fastqc-2.out-mode {
                alias:fasqc3_out_dir_type;
            }
            fastqc-3.custom-dir {
                alias:fasqc4_out_dir;
            }
            fastqc-3.out-mode {
                alias:fasqc4_out_dir_type;
            }
        }
        visual {
            CASAVAFilter {
                pos:"-1230 -555";
                style:ext;
                bg-color-ext:"194 0 0 64";
                bounds:"-30 -30 123.875 82";
                in-file.angle:97.4959;
                out-file.angle:268.768;
            }
            CASAVAFilter-1 {
                pos:"-720 -930";
                style:ext;
                bg-color-ext:"194 0 0 64";
                bounds:"-30 -30 119.875 81";
                in-file.angle:181.79;
                out-file.angle:359.076;
            }
            CutAdaptFastq {
                pos:"-495 -825";
                style:ext;
                bg-color-ext:"236 177 178 64";
                in-file.angle:49.8991;
                out-file.angle:344.434;
            }
            CutAdaptFastq-1 {
                pos:"-1110 -330";
                style:ext;
                bg-color-ext:"236 177 178 64";
                in-file.angle:34.1145;
                out-file.angle:351.588;
            }
            MergeFastq {
                pos:"-435 -210";
                style:simple;
                bg-color-simple:"78 151 184 255";
                in-file.angle:171.87;
                out-file.angle:1.4688;
            }
            MergeFastq-1 {
                pos:"-165 -435";
                style:simple;
                bg-color-simple:"78 151 184 255";
                in-file.angle:91.9092;
                out-file.angle:271.432;
            }
            QualityTrim {
                pos:"-825 -255";
                style:ext;
                bg-color-ext:"204 68 102 64";
                in-file.angle:211.827;
                out-file.angle:347.391;
            }
            QualityTrim-1 {
                pos:"-210 -705";
                style:ext;
                bg-color-ext:"204 68 102 64";
                bounds:"-30 -30 107.125 96";
                in-file.angle:188.13;
                out-file.angle:292.859;
            }
            fastqc {
                pos:"-870 -780";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:90;
            }
            fastqc-1 {
                pos:"-1035 -705";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:180;
            }
            fastqc-2 {
                pos:"0 -390";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:180;
            }
            fastqc-2-1 {
                pos:"-285 -555";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:180;
            }
            fastqc-3 {
                pos:"-405 -75";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:88.0251;
            }
            get-file-list {
                pos:"-1290 -795";
                style:ext;
                bg-color-ext:"24 102 175 64";
                bounds:"-30 -30 87.25 90";
                out-url.angle:296.095;
            }
            get-file-list-1 {
                pos:"-960 -975";
                style:ext;
                bg-color-ext:"24 102 175 64";
                bounds:"-30 -30 86 92";
                out-url.angle:328.062;
            }
            multiplexer {
                pos:"-165 -210";
                style:simple;
                bg-color-simple:"84 84 84 255";
                input-data-1.angle:186.911;
                input-data-2.angle:88.2643;
                output-data.angle:145.62;
            }
            tophat {
                pos:"-570 -510";
                style:ext;
                bg-color-ext:"0 128 0 64";
                bounds:"-30 -30 140.375 90";
                in-sequence.angle:327.046;
                out-assembly.angle:11.0864;
            }
            CASAVAFilter-1.out-file->CutAdaptFastq.in-file {
                text-pos:"-1.75 -27";
            }
            CASAVAFilter.out-file->CutAdaptFastq-1.in-file {
                text-pos:"-35.75 -24";
            }
            CutAdaptFastq-1.out-file->QualityTrim.in-file {
                text-pos:"-35.75 -24";
            }
            CutAdaptFastq.out-file->QualityTrim-1.in-file {
                text-pos:"-39.75 -10";
            }
            MergeFastq-1.out-file->fastqc-2.in-file {
                text-pos:"-34.75 -28";
            }
            MergeFastq-1.out-file->multiplexer.input-data-2 {
                text-pos:"-2.75 -17";
            }
            MergeFastq.out-file->fastqc-3.in-file {
                text-pos:"-47.75 1";
            }
            MergeFastq.out-file->multiplexer.input-data-1 {
                text-pos:"-31.75 -26";
            }
            QualityTrim-1.out-file->MergeFastq-1.in-file {
                text-pos:"-48.75 -13";
            }
            QualityTrim.out-file->MergeFastq.in-file {
                text-pos:"-35.75 -26";
            }
            get-file-list-1.out-url->CASAVAFilter-1.in-file {
                text-pos:"-38.7578 -25";
            }
            get-file-list-1.out-url->fastqc.in-file {
                text-pos:"-31.7578 -14";
            }
            get-file-list.out-url->CASAVAFilter.in-file {
                text-pos:"-39.7578 -13";
            }
            get-file-list.out-url->fastqc-1.in-file {
                text-pos:"-28.7578 -27";
            }
            multiplexer.output-data->tophat.in-sequence {
                text-pos:"-111 -64";
            }
            tophat.out-assembly->fastqc-2-1.in-file {
                text-pos:"-44.2266 -24";
            }
        }
        wizard {
            name:"Raw RNA-Seq Data Processing Wizard";
            page {
                id:1;
                next:2;
                title:"Input data";
                parameters-area {
                    group {
                        title:"Sequencing reads";
                        label-size:120;
                        get-file-list.url-in {
                            label:"FASTQ files";
                        }
                        get-file-list-1.url-in {
                            label:"FASTQ files with pairs";
                        }
                    }
                }
            }
            page {
                id:2;
                next:3;
                title:Pre-processing;
                parameters-area {
                    group {
                        title:"Reads filtration";
                        label-size:120;
                        QualityTrim.qual-id {
                        }
                        QualityTrim.len-id {
                            label:"Min length";
                        }
                        QualityTrim.both-ends {
                            label:"Trim both ends";
                        }
                        CutAdaptFastq.adapters-url {
                            label:"3' adapters";
                        }
                        CutAdaptFastq.front-url {
                            label:"5' adapters";
                        }
                        CutAdaptFastq.anywhere-url {
                            label:"5' and 3' adapters";
                        }
                    }
                    group {
                        title:"Read pairs filtration";
                        label-size:120;
                        QualityTrim-1.qual-id {
                        }
                        QualityTrim-1.len-id {
                            label:"Min length";
                        }
                        QualityTrim-1.both-ends {
                            label:"Trim both ends";
                        }
                        CutAdaptFastq-1.adapters-url {
                            label:"3' adapters";
                        }
                        CutAdaptFastq-1.front-url {
                            label:"5' adapters";
                        }
                        CutAdaptFastq-1.anywhere-url {
                            label:"5' and 3' adapters";
                        }
                    }
                }
            }
            page {
                id:3;
                next:4;
                title:Mapping;
                parameters-area {
                    group {
                        title:"TopHat input";
                        label-size:180;
                        bowtie-index {
                            tophat.bowtie-index-dir {
                            }
                            tophat.bowtie-index-basename {
                            }
                        }
                        tophat.bowtie-version {
                        }
                    }
                    group {
                        title:Parameters;
                        label-size:170;
                        tophat.known-transcript {
                        }
                        tophat.raw-junctions {
                        }
                    }
                    group {
                        title:Additional;
                        label-size:170;
                        type:hideable;
                        tophat.mate-inner-distance {
                        }
                        tophat.mate-standard-deviation {
                        }
                        tophat.library-type {
                        }
                        tophat.no-novel-junctions {
                        }
                        tophat.max-multihits {
                        }
                        tophat.segment-length {
                        }
                        tophat.fusion-search {
                        }
                        tophat.transcriptome-only {
                        }
                        tophat.transcriptome-max-hits {
                        }
                        tophat.prefilter-multihits {
                        }
                        tophat.min-anchor-length {
                        }
                        tophat.splice-mismatches {
                        }
                        tophat.read-mismatches {
                        }
                        tophat.segment-mismatches {
                        }
                        tophat.solexa-1-3-quals {
                        }
                        tophat.bowtie-n-mode {
                        }
                        tophat.bowtie-tool-path {
                        }
                        tophat.samtools-tool-path {
                        }
                        tophat.path {
                        }
                        tophat.temp-dir {
                        }
                    }
                }
            }
            page {
                id:4;
                title:"Output data";
                parameters-area {
                    group {
                        title:"TopHat data";
                        label-size:130;
                        tophat.out-dir {
                            label:Tophat;
                        }
                    }
                    group {
                        title:"Filtered FASTQ";
                        label-size:130;
                        type:hideable;
                        CASAVAFilter.out-mode {
                        }
                        CASAVAFilter.custom-dir {
                        }
                    }
                    group {
                        title:"Filtered FASTQ with pairs";
                        label-size:130;
                        type:hideable;
                        CASAVAFilter-1.out-mode {
                        }
                        CASAVAFilter-1.custom-dir {
                        }
                    }
                }
            }
        }
    }
}