DIMS.config

params {
    scripts_dir = "$projectDir/CustomModules/DIMS/Utils/" 
    tools_dir = "/hpc/dbg_mz/tools/db"
    hmdb_db_file = "$params.tools_dir/HMDB_V5/HMDB_V5_iso_adducts_IS.RData"
    relevance_file = "$params.tools_dir/HMDB_V5/HMDB_V5_iso_adducts_IS_rlvnc.RData"
    hmdb_parts_files = "$params.tools_dir/HMDB_V5/hmdb_parts/"
    sst_components_file = "$params.tools_dir/SST_componenten.txt"
    path_metabolite_groups = "$params.tools_dir/HMDB_V5/metabolite_groups"
    file_ratios_metabolites = "$params.tools_dir/HMDB_V5/Ratios_between_metabolites.csv"
    file_expected_biomarkers_IEM = "$params.tools_dir/HMDB_V5/Expected_biomarkers_IEM_V5.csv"
    file_explanation = "/hpc/dbg_mz/tools/Explanation_violin_plots.txt"
    file_isomers = "/hpc/dbg_mz/tools/isomers.txt"
    trim = 0.1
    thresh = 2000
    cluster_options = "--mail-user $params.email --mail-type FAIL --account=dbg_mz"
}

process {
    withLabel: AssignToBins {
        cpus = 2
        memory = { 3.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: AverageTechReplicates {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time =  { 30.m * task.attempt }
        publishDir = [
            [
                path: "$params.outdir/Bioinformatics",
                mode: 'link',
                pattern: '*.txt'
            ],
            [
                path: "$params.outdir/Bioinformatics",
                mode: 'link',
                pattern: '*.pdf'
            ],
            [
                path: "$params.outdir/Bioinformatics/RData",
                mode: 'link',
                pattern: '*repl_pattern.RData'
            ]
        ]
    }

    withLabel: CollectFilled {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 5.m * task.attempt }
        publishDir = [
            [
                path: "$params.outdir/Bioinformatics",
                mode: 'link',
                pattern: 'outlist_identified_*.txt'
            ],
            [
                path: "$params.outdir/Bioinformatics/RData",
                mode: 'link',
                pattern: 'outlist_identified_*.RData'
            ]
        ]
    }
    
    withLabel: CollectSumAdducts {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/Bioinformatics/RData"
            mode = 'link'
            pattern = 'AdductSums*.RData'
        }
    }

    withLabel: FillMissing {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: GenerateBreaks {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time =  { 10.m * task.attempt }
    }

    withLabel: GenerateExcel {
        cpus = 2
        memory = { 10.GB * task.attempt }
        time = { 10.m * task.attempt }
        publishDir = [
            [
                path: "$params.outdir/Bioinformatics/RData", 
                mode: 'link', 
                pattern: '*.RData'
            ],
            [
                path: "$params.outdir/Bioinformatics", 
                mode: 'link', 
                pattern: '*.txt'
            ],
            [
                path: "$params.outdir/Bioinformatics", 
                mode: 'link', 
                pattern: '*.xlsx'
            ],
            [
                path: "$params.outdir/Bioinformatics", 
                mode: 'link', 
                pattern: 'plots/*.png'
            ]
        ]
    }

    withLabel: GenerateViolinPlots {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 20.m * task.attempt }
        publishDir = [
            [
                path: "$params.outdir/Bioinformatics/dIEM",
                mode: 'link',
                pattern: '*.xlsx'
            ],
            [
                path: "$params.outdir/Bioinformatics/dIEM",
                mode: 'link',
                pattern: 'Diagnostics/*.pdf'
            ],
            [
                path: "$params.outdir/Bioinformatics/dIEM",
                mode: 'link',
                pattern: 'Other/*.pdf'
            ],
            [
                path: "$params.outdir/Bioinformatics/dIEM",
                mode: 'link',
                pattern: 'dIEM_plots/*.pdf'
            ],
            [
                path: "$params.outdir/Bioinformatics",
                mode: 'link',
                pattern: '*.txt'
            ],
            [
                path: "$params.outdir/Bioinformatics",
                mode: 'link',
                pattern: '*.csv'
            ]
        ]
    }

    withLabel: HMDBparts {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 60.m * task.attempt }
    }

    withLabel: HMDBparts_main {
        cpus = 2
        memory = { 4.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: PeakFinding {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 20.m * task.attempt }
    }

    withLabel: PeakGrouping {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 80.m * task.attempt }
    }

    withLabel: SpectrumPeakFinding {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: SumAdducts {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { 40.m * task.attempt }
    }

    withLabel: ThermoRawFileParser_1_1_11 {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: UnidentifiedCalcZscores {
        cpus = 2
        memory = { 10.GB * task.attempt }
        time = { 10.m * task.attempt }

        publishDir {
            path = "$params.outdir/Bioinformatics/RData"
            mode = 'link'
            pattern = '*.RData'
        }
    }

    withLabel: UnidentifiedCollectPeaks {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: UnidentifiedFillMissing {
        cpus = 2
        memory = { 10.GB * task.attempt }
        time = { 15.m * task.attempt }
    }

    withLabel: UnidentifiedPeakGrouping {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { 300.m * task.attempt }
    }

    withLabel: VersionLog {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/Bioinformatics/log"
            mode = 'link'
        }
    }

    withLabel: Workflow_Export_Params {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/Bioinformatics/log"
            mode = 'link'
        }
    }
}

report {
    enabled = true
    file = "$params.outdir/log/nextflow_report.html"
}

trace {
    enabled = true
    overwrite = true
    file = "$params.outdir/log/nextflow_trace.txt"
    fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem'
}

timeline {
    enabled = true
    file = "$params.outdir/log/nextflow_timeline.html"
}

profiles {

    slurm {
        process {
            executor = 'slurm'
            queue = 'cpu'
            clusterOptions = "$params.cluster_options"
            errorStrategy = 'retry'
            maxRetries = 2
        }

        singularity {
            enabled = true
            runOptions = '-B /hpc/dbg_mz:/hpc/dbg_mz -B $TMPDIR:$TMPDIR'
            autoMounts = true
            cacheDir = '/hpc/dbg_mz/tools/singularity_cache'
        }

        executor {
            queueSize = 1000
            pollInterval = '1min'
            queueStatInterval = '5min'
            submitRatelimit = '10sec'
        }

        mail {
            smtp.host = 'localhost'
        }
    }
}