TCRtoolkit/nextflow.config at main · KarchinLab/TCRtoolkit · GitHub

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// bulk.config

docker {
    enabled = true
}

plugins {
    id 'nf-schema@2.7.2'
}

params {
    samplesheet = null
    outdir = 'out'
    sobject_gex = null // specify filepath if pseudobulking by phenotype

    publish_dir_mode           = 'copy'

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory                 = 768.GB
    max_cpus                   = 192
    max_time                   = 48.h

    input_format = "airr" // cellranger, adaptive
    airr_schema = "${projectDir}/assets/airr/airr_rearrangement_schema.json"
    imgt_lookup = "${projectDir}/assets/airr/imgt_adaptive_lookup.tsv"

    // Sample + compare parameters
    workflow_level = "sample,compare"
    project_name = "tcrtoolkit_"+ new Date().format("yyyy-MM-dd_HH-mm-ss")
    sample_stats_template = "${projectDir}/notebooks/sample_stats_template.qmd"
    compare_stats_template = "${projectDir}/notebooks/compare_stats_template.qmd"

    // Sample stats metadata parameters
    samplechart_x_col = 'timepoint'
    samplechart_color_col = 'origin'
    vgene_subject_col = 'patient'
    vgene_x_cols = 'origin,timepoint'

    // Notebooks parameters
    timepoint_col = 'timepoint'
    timepoint_order_col = 'timepoint_order'
    alias_col = 'alias'
    subject_col = 'patient'

    // OLGA parameters
    olga_chunk_length = 100000 // larger chunk size = less parallelization

    // GIANA parameters
    threshold = 7.0
    threshold_score = 3.6
    threshold_vgene = 3.7

    // GLIPH2 parameters
    use_gliph2 = true
    gliph2_report_template = "${projectDir}/notebooks/gliph2_report_template.qmd"
    ref_files = "${projectDir}/assets/gliph2_files"

    local_min_pvalue = "0.001"
    p_depth = "1000"
    global_convergence_cutoff = "1"
    simulation_depth = "1000"
    kmer_min_depth = "3"
    local_min_OVE = "c(1000, 100, 10)"
    algorithm = "GLIPH2"
    all_aa_interchangeable = "1"

    // TCRDIST3 parameters
    matrix_sparsity = "sparse"
    distance_metric = "tcrdist"
    db_path = "${projectDir}/assets/tcrdist3_files/alphabeta_gammadelta_db.tsv"

    //container to use for running the workflow
    container = "ghcr.io/karchinlab/tcrtoolkit:main"

    //reports
    template_qc = "${projectDir}/notebooks/template_qc.qmd"
}

includeConfig 'conf/base.config'
includeConfig 'conf/modules.config'