nextflow.config

manifest {
    description = 'PhIP-Seq common analysis workflows'
    nextflowVersion = '>= 20.07.0'
}

params{
    //  Set this as 'cat' if fastq files not g'zipped
    fastq_stream_func = 'zcat'

    /*
    output options
    */

    //  Dataset Name Prefix 
    dataset_prefix = 'data'

    // Output Xarray pickle
    output_pickle_xarray = false

    //  Output tall format ds 
    output_tall_csv = false

    //  Output wide format ds 
    output_wide_csv = true

    // Add FHIR reporting option
    output_fhir_report = false

    /*
    alignment options
    */

    // other bowtie options
    bowtie_optional_args = '--local --very-sensitive-local'

    // Flag for replicating counts for replicate sequences
    replicate_sequence_counts = true

    /*
    Optional workflows
    */

    run_cpm_enr_workflow = true
    run_zscore_fit_predict = true
    run_zscore_fdr_analysis = true
    run_virus_score_analysis = true
    run_edgeR = false
    run_BEER = false
    run_streamlit = true     

    // Virus score calculation parameters
    virus_score_level = 'Species'
    virus_score_epitope_len = 7

    /*
    Options for grouping results by organism (e.g. VirScan)
    */

    // Flag used to control the summary of results by organism
    summarize_by_organism = false

    // Column in the peptide table indicating the organism for each peptide
    peptide_org_col = "Organism"

    // Column in the peptide table containing the peptide sequence
    // (used to match against public epitopes, and to filter overlapping peptides)
    peptide_seq_col = "Sequence"

    // Maximum allowed overlap between detected peptides
    max_overlap = 7

    // Minimum z-score threshold
    zscore_threshold = 3.5

    // Maximum edgeR threshold (BH-adjusted p-value)
    edgeR_threshold = 0.05

    // Column in the sample table used for mapping replicates to samples
    sample_grouping_col = ""

    // Optional, a CSV containing public epitopes
    public_epitopes_csv = "$baseDir/templates/public_epitope_template.csv"

    // In the public epitopes CSV, the column containing the translated amino acid sequence
    public_epitopes_col = "peptide_translate"

    // 3D structure paths
    pdb_dir = "$baseDir/data/VIR3-example/pdb_structures/"

    // Input Files
    sample_table     = "$baseDir/data/VIR3-example/sample_table_with_beads_no_lib.csv"
    peptide_table    = "$baseDir/data/VIR3-example/peptide_table_with_pdb.csv"
    oligo_metadata   = "$baseDir/data/VIR3-example/peptide_table_with_pdb.csv"
    
    // Flow control parameters
    reads_prefix     = "$baseDir"
    results          = "$baseDir/results/"
    deploy_streamlit = true
    streamlit_port   = 8501
    version          = "0.5.0"

    // IEDB annotation parameters
    iedb_database = "$baseDir/data/VIR3-example/epitope_full_v3.tsv"
    epitope_length_min = 4    
    epitope_length_max = 35
    max_workers = 4  
    chunk_size = 100  

    // Neutralization scoring (experimental)
    neutralization_threshold     = 3.0
    conservation_weight          = 0.15
    phip_signal_weight           = 0.25
    iedb_evidence_weight         = 0.10
    neutralization_db_weight     = 0.25
    epitope_coverage_weight      = 0.15
    bfactor_weight               = 0.10
    sasa_buried_threshold        = 0.2
    spatial_cluster_angstrom     = 8.0
    neutralization_db            = "$baseDir/data/VIR3-example/epitope_neutralizing_all_linear.tsv"

}

process {

    // Default for any processes which do not match the selectors below
    container = 'quay.io/matsengrp/phip-flow:latest'

    withName: 'run_edgeR|run_BEER' {
        container = 'quay.io/biocontainers/bioconductor-beer:1.2.0--r42hdfd78af_0'
    }

}

profiles {

    standard {
    }
   
    docker {
        docker.enabled = true
    }

    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        singularity.runOptions = '--contain -W /tmp/ -B ${HOME},${PWD}'
    }

    apptainer {
        apptainer.enabled = true
        apptainer.autoMounts = true
        apptainer.runOptions = '--contain -W /tmp/ -B ${HOME},${PWD}'
    }
 
    cluster {

        singularity {
            enabled = true
            autoMounts = true
            cacheDir = 'singularity_cache' 
            runOptions = '--contain -W /tmp/ -B ${HOME},${PWD}'
        }

        process {
            executor = 'slurm'
            queue = 'campus-new'
            cpus = 1
            memory = 16.GB
            time = '1h'
            clusterOptions = '-A overbaugh_j'
            withLabel: mem_large { memory = 48.GB }
            withLabel: mem_xlarge { memory = 64.GB }
        }
    }
}

report {
    enabled = true
    file = "$baseDir/results/reports/execution.html"
    overwrite = true
}

timeline {
    enabled = true
    file = "$baseDir/results/reports/timeline.html"
    overwrite = true
}

dag {
    enabled = true
    file = "$baseDir/results/reports/dag.html"
    overwrite = true
}