#@UGENE_WORKFLOW
#The workflow takes FASTQ files as input and process this data as follows:
#  * Pre-processing:
#    - Filtration of the input sequencing reads by the CASAVA header (for Illumina platform).
#    - Cutting of adapter sequences.
#    - Trimming of the sequencing reads by quality.
#
#  * Mapping:
#    - Mapping of the reads to a reference sequence (the BWA-MEM tool is used).
#
#  * Post-processing:
#    - Merging of all data into one file.
#    - Filtration of aligned reads by SAMtools to remove reads with low mapping quality, unpaired/unaligned reads, etc.
#    - Removing of PCR duplicates.
#
#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 filtered, sorted, and indexed BAM file.
#

workflow "Raw DNA-Seq data processing" {
    .meta {
        wizard {
            help-page-id:16122726;
            auto-run: true;
            has-run-button: false;
            has-defaults-button: false;
            name: "Configure Raw DNA-Seq Data Processing";
            finish-label: "Setup";
            result {
                NGS/raw_ngs/dnaseq/dna_single.uwl: pipeline.single;
                NGS/raw_ngs/dnaseq/dna_paired.uwl: pipeline.paired;
            }
            page {
                id: 1;
                title: "General settings";
                parameters-area {
                    group {
                        title:"Sequencing reads";
                        radio {
                            id: pipeline;
                            value {
                                id: single;
                                label: "Single-end";
                            }
                            value {
                                id: paired;
                                label: "Paired-end";
                            }
                        }
                    }
                }
            }
        }
    }
}