#@UGENE_WORKFLOW
#The workflow takes FASTQ files (with single-end sequencing reads) 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.
#
#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 of the workflow running is a merged FASTQ file.
#



workflow "Processing of raw RNA-Seq single-end reads"{

    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;
        out-mode:0;
        len-id:10;
        qual-id:20;
    }
    get-file-list {
        type:get-file-list;
        name:"Read FASTQ Files with Reads";
        url-in {
            dataset:"Dataset 1";
        }
    }
    MergeFastq {
        type:MergeFastq;
        name:"Merge FASTQ Files";
        custom-dir:filtered_fastq;
        out-mode:0;
        out-name:in_1.fq;
    }
    CutAdaptFastq {
        type:CutAdaptFastq;
        name:"Cut Adapter";
        out-mode:0;
    }
    fastqc {
        type:fastqc;
        name:"FastQC Quality Control";
        out-mode:1;
    }
    fastqc-1 {
        type:fastqc;
        name:"FastQC Quality Control";
        out-mode:1;
    }

    .actor-bindings {
        get-file-list.out-url->CASAVAFilter.in-file
        get-file-list.out-url->fastqc.in-file
        CutAdaptFastq.out-file->QualityTrim.in-file
        CASAVAFilter.out-file->CutAdaptFastq.in-file
        QualityTrim.out-file->MergeFastq.in-file
        QualityTrim.out-file->fastqc-1.in-file
    }

    get-file-list.url->CASAVAFilter.in-file.url
    CutAdaptFastq.url->QualityTrim.in-file.url
    QualityTrim.url->MergeFastq.in-file.url
    CASAVAFilter.url->CutAdaptFastq.in-file.url
    get-file-list.url->fastqc.in-file.url
    QualityTrim.url->fastqc-1.in-file.url

    .meta {
        parameter-aliases {
            CASAVAFilter.out-mode {
                alias:out_mode;
            }
            get-file-list.url-in {
                alias:in;
            }
        }
        visual {
            CASAVAFilter {
                pos:"-840 -536";
                style:ext;
                bg-color-ext:"194 0 0 64";
                bounds:"-30 -30 179.875 92";
                in-file.angle:180;
                out-file.angle:360;
            }
            CutAdaptFastq {
                pos:"-525 -534";
                style:ext;
                bg-color-ext:"236 177 178 64";
                bounds:"-30 -30 173.25 95";
                in-file.angle:180;
                out-file.angle:303.69;
            }
            MergeFastq {
                pos:"-475 -103";
                style:simple;
                bg-color-simple:"78 151 184 255";
                in-file.angle:90;
                out-file.angle:251.565;
            }
            QualityTrim {
                pos:"-500 -327";
                style:ext;
                bg-color-ext:"204 68 102 64";
                bounds:"-30 -30 140 96";
                in-file.angle:37.5041;
                out-file.angle:293.86;
            }
            fastqc {
                pos:"-871 -329";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:128.047;
            }
            fastqc-1 {
                pos:"-307 -26";
                style:simple;
                bg-color-simple:"0 128 128 255";
                in-file.angle:149.744;
            }
            get-file-list {
                pos:"-1055 -536";
                style:ext;
                bg-color-ext:"24 102 175 64";
                bounds:"-30 -30 74.25 92";
                out-url.angle:360;
            }
            CASAVAFilter.out-file->CutAdaptFastq.in-file {
                text-pos:"-38.75 -27";
            }
            CutAdaptFastq.out-file->QualityTrim.in-file {
                text-pos:"-41.75 -18";
            }
            QualityTrim.out-file->MergeFastq.in-file {
                text-pos:"-60.75 -3";
            }
            QualityTrim.out-file->fastqc-1.in-file {
                text-pos:"0.25 7";
            }
            get-file-list.out-url->CASAVAFilter.in-file {
                text-pos:"-36.7578 -28";
            }
            get-file-list.out-url->fastqc.in-file {
                text-pos:"-33.7578 26";
            }
        }
        wizard {
            name:"Raw RNA-Seq Data Processing Wizard";
            help-page-id:16122727;
            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";
                        }
                    }
                }
            }
            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";
                        }
                    }
                }
            }
            page {
                id:3;
                title:"Output data";
                parameters-area {
                    group {
                        title:"Filtered FASTQ";
                        label-size:130;
                        type:hideable;
                        CASAVAFilter.out-mode {
                        }
                        CASAVAFilter.custom-dir {
                        }
                    }
                }
            }
        }
    }
}