#@UGENE_WORKFLOW
#The workflow takes FASTQ files with metagenomic NGS reads as input and process them as follows:
# * Improve reads quality with Trimmomatic
# * Provide FastQC reads quality reports
# * Classification:
#   - Classify the pre-processed reads with Kraken.
#   - Classify these reads with CLARK.
#   - Classify these reads with DIAMOND (in case of SE reads).
#   - Classify these reads with MetaPhlAn2.
#   - Ensemble the classification output from Kraken, CLARK, and DIAMOND into a CSV file.
#   - Improve classification from these tools with WEVOTE.
#   - Provide general classification reports.

workflow "Parallel NGS reads classification" {
    .meta {
        wizard {
            auto-run: true;
            has-run-button: false;
            has-defaults-button: false;
            name: "Configure Parallel NGS Reads Classification";
            finish-label: "Setup";
            result {
                NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_single.uwl: pipeline.single;
                NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_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";
                            }
                        }
                    }
                }
            }
        }
    }

}