nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/pixelator Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/


// Global default params, used in configs
params {

    // Input options
    input                                                   = null
    input_basedir                                           = null

    // Main pixelator container override
    pixelator_container                                     = null
    experiment_summary_container                            = null



    /*
    ===============================================================
        PNA options
    ===============================================================
    */
    save_pna_amplicon_reads                                 = false
    save_pna_demux_parquet                                  = false
    save_pna_demux_passed_reads                             = false
    save_pna_demux_failed_reads                             = false
    save_pna_collapsed_reads                                = false
    save_pna_graph_pixelfile                                = false
    save_pna_sample_calling_pixelfile                       = false
    save_pna_denoise_pixelfile                              = false
    save_pna_analysis_pixelfile                             = false

    technology                                              = null

    // PNA amplicon
    pna_amplicon_mismatches                                 = 0.1
    pna_amplicon_remove_polyg                               = true
    pna_amplicon_quality_cutoff                             = 20
    pna_amplicon_low_complexity_filter                      = true
    pna_amplicon_low_complexity_threshold                   = 0.8
    pna_amplicon_lbs_filter                                 = true
    pna_amplicon_lbs_filter_min_overlap                     = 8
    pna_amplicon_lbs_filter_error_rate                      = 0.1


    // PNA demux
    pna_demux_mismatches                                    = 1
    pna_demux_output_chunk_reads                            = '50M'
    pna_demux_output_max_chunks                             = 8
    pna_demux_strategy                                      = "independent"

    // PNA collapse
    pna_collapse_mismatches                                 = 2
    pna_collapse_algorithm                                  = 'directional'

    // PNA graph
    pna_graph_multiplet_recovery                            = true
    pna_graph_initial_stage_leiden_resolution               = 1.0
    pna_graph_refinement_stage_leiden_resolution            = 0.01
    pna_graph_min_count                                     = 1
    pna_graph_max_refinement_recursion_depth                = 3
    pna_graph_edge_cycle_verification                       = true
    pna_graph_initial_stage_max_edges_to_remove             = 10
    pna_graph_refinement_stage_max_edges_to_remove          = 10
    pna_graph_initial_stage_max_edges_to_remove_relative    = null
    pna_graph_refinement_stage_max_edges_to_remove_relative = null
    pna_graph_component_size_min_threshold                  = 8000

    // sample-calling options
    pna_sample_calling_remove_incompatible     = true
    pna_sample_calling_save_undetermined       = false
    pna_sample_calling_confidence_threshold    = 0.9

    // PNA denoise
    pna_denoise_run_one_core_graph_denoising                = false
    pna_denoise_pval_threshold                              = 0.05
    pna_denoise_inflate_factor                              = 1.5
    pna_denoise_run_ace_denoising                           = true
    pna_denoise_ace_k                                       = 3
    pna_denoise_run_pls_denoising                           = true
    pna_denoise_pls_score_threshold                         = -3.0
    skip_denoise                                            = false

    // PNA analysis
    pna_analysis_compute_proximity                          = true
    pna_analysis_proximity_nbr_of_permutations              = 100
    pna_analysis_compute_k_cores                            = true
    pna_analysis_compute_svd_var_explained                  = true
    pna_analysis_svd_nbr_of_pivots                          = 50
    skip_analysis                                           = false

    // PNA layout
    pna_layout_no_node_marker_counts                        = false
    pna_layout_layout_algorithm                             = "wpmds_3d"
    pna_layout_pmds_pivots                                  = 50
    pna_layout_wpmds_k                                      = 5
    skip_layout                                             = false

    // Experiment summary
    skip_experiment_summary                                 = false

    // Common output options
    save_json                                               = true
    save_all                                                = false

    // Boilerplate options
    outdir                                                  = null
    publish_dir_mode                                        = 'copy'
    email                                                   = null
    email_on_fail                                           = null
    plaintext_email                                         = false
    monochrome_logs                                         = false
    help                                                    = false
    help_full                                               = false
    show_hidden                                             = false
    version                                                 = false
    pipelines_testdata_base_path                            = System.getenv('NFT_TESTDATA_BASE_PATH') ?: 'https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/'
    modules_testdata_base_path                              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
    trace_report_suffix                                     = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')

    // Config options
    config_profile_name                                     = null
    config_profile_description                              = null

    custom_config_version                                   = 'master'
    custom_config_base                                      = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact                                  = null
    config_profile_url                                      = null

    // Schema validation default options
    validate_params                                         = true
}

// Backwards compatibility for publishDir syntax
outputDir = params.outdir
workflow.output.mode = params.publish_dir_mode

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug {
        dumpHashes                                   = true
        process.beforeScript                         = 'echo $HOSTNAME'
        cleanup                                      = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled        = true
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        conda.channels       = ['conda-forge', 'bioconda']
        apptainer.enabled    = false
    }
    mamba {
        conda.enabled        = true
        conda.useMamba       = true
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        apptainer.enabled    = false
    }
    docker {
        docker.enabled       = true
        conda.enabled        = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        apptainer.enabled    = false
        docker.runOptions    = '-u $(id -u):$(id -g)'
        includeConfig 'conf/container_env.config'
    }
    arm64 {
        process.arch            = 'arm64'
        // TODO https://github.com/nf-core/modules/issues/6694
        // For now if you're using arm64 you have to use wave for the sake of the maintainers
        // wave profile
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    emulate_amd64 {
        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        includeConfig 'conf/container_env.config'
    }
    podman {
        podman.enabled       = true
        conda.enabled        = false
        docker.enabled       = false
        singularity.enabled  = false
        shifter.enabled      = false
        charliecloud.enabled = false
        apptainer.enabled    = false
        podman.runOptions    = '--userns=keep-id'
        includeConfig 'conf/container_env.config'
    }
    shifter {
        shifter.enabled      = true
        conda.enabled        = false
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        charliecloud.enabled = false
        apptainer.enabled    = false
        includeConfig 'conf/container_env.config'
    }
    charliecloud {
        charliecloud.enabled = true
        conda.enabled        = false
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        apptainer.enabled    = false
        includeConfig 'conf/container_env.config'
    }
    apptainer {
        apptainer.enabled    = true
        apptainer.autoMounts = true
        conda.enabled        = false
        docker.enabled       = false
        singularity.enabled  = false
        podman.enabled       = false
        shifter.enabled      = false
        charliecloud.enabled = false
        includeConfig 'conf/container_env.config'
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gpu {
        docker.runOptions      = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions   = '--nv'
        singularity.runOptions = '--nv'
    }

    test {
        includeConfig 'conf/test.config'
    }

    test_proxiome_v1 {
        includeConfig 'conf/test_proxiome_v1.config'
    }

    test_proxiome_v2 {
        includeConfig 'conf/test_proxiome_v2.config'
    }

    test_full {
        includeConfig 'conf/test_full.config'
    }

    cells_1k {
        includeConfig 'conf/cells_1k.config'
    }

    cells_8k {
        includeConfig 'conf/cells_8k.config'
    }
}
// Load nf-core custom profiles from different institutions
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry    = 'quay.io'
docker.registry       = 'quay.io'
podman.registry       = 'quay.io'
singularity.registry  = 'quay.io'
charliecloud.registry = 'quay.io'

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'nf-core/pixelator'
    // Keep both author and contributors fields for compatibility with Nextflow versions < 24.10.0
    author          = """Pixelgen Technologies AB"""
    // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
    contributors    = [
        [
            name: 'Florian De Temmerman',
            affiliation: 'Pixelgen Technologies AB',
            email: 'florian.detemmerman@pixelgen.com',
            github: '@fbdtemme',
            contribution: ["author", "maintainer"],
            orcid: '0009-0006-0086-2470',
        ],
        [
            name: 'Johan Dahlberg',
            affiliation: 'Pixelgen Technologies AB',
            email: 'johan.dahlberg@pixelgen.com',
            github: '@johandahlberg',
            contribution: ["contributor"],
            orcid: '0000-0001-6962-1460',
        ],
        [
            name: 'Alvaro Martinez Barrio',
            affiliation: 'Pixelgen Technologies AB',
            email: 'alvaro.martinez.barrio@pixelgen.com',
            github: '@ambarrio',
            contribution: ["contributor"],
            orcid: '0000-0001-5064-2093',
        ],
    ]

    homePage        = 'https://github.com/nf-core/pixelator'
    description     = """Pipeline for analysis of Proximity Network Assay data"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.4'
    version         = '4.1.1'
    doi             = '10.1101/2023.06.05.543770'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.7.2'
    id 'nf-slack@0.5.1'
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs      = params.monochrome_logs
}

slack {
    enabled = true
    webhook {
        url = System.getenv('HOOK_URL')
    }
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
includeConfig 'conf/modules.pna.config'