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

// Global default params, used in configs
params {

    // Input options
    input                      = null

    // Pipeline parameters
    // QC
    skip_preprocessing                           = false
    min_seq_length                               = 30
    max_seq_length                               = 5000
    remove_duplicates_on_sequence                = false
    // Clustering
    save_mmseqs_db                               = false
    clustering_tool                              = 'cluster'
    cluster_seq_identity                         = 0.3
    cluster_coverage                             = 0.5
    cluster_cov_mode                             = 0
    save_mmseqs_clustering                       = false
    cluster_size_threshold                       = 25
    save_mmseqs_chunked_fasta                    = false
    // Alignment
    alignment_tool                               = 'famsa'
    skip_msa_trimming                            = false
    clipkit_out_format                           = 'clipkit'
    trim_ends_only                               = true
    gap_threshold                                = 0.5
    skip_additional_sequence_recruiting          = false
    hmmsearch_write_target                       = false
    hmmsearch_write_domain                       = true
    hmmsearch_evalue_cutoff                      = 0.001
    save_hmmsearch_results                       = false
    hmmsearch_query_length_threshold             = 0.9
    save_hmmsearch_filtered_fasta                = false
    // Redundancy
    skip_family_redundancy_removal               = false
    skip_family_merging                          = false
    hmmsearch_family_redundancy_length_threshold = 1
    hmmsearch_family_similarity_length_threshold = 0.9
    save_non_redundant_fams_fasta                = false
    skip_sequence_redundancy_removal             = false
    cluster_seq_identity_for_redundancy          = 0.9
    cluster_coverage_for_redundancy              = 0.9
    cluster_cov_mode_for_redundancy              = 0
    save_non_redundant_seqs_fasta                = true
    // Downstream samplesheets
    skip_proteinfold_samplesheet                 = true

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                       = null
    publish_dir_mode             = 'copy'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    hook_url                     = System.getenv('HOOK_URL')
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteinfamilies/'
    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
    modules_testdata_base_path = null

    // Schema validation default options
    validate_params            = true
}

// 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)'
    }
    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
    }
    podman {
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter {
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    charliecloud {
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    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
    }
    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_minimal              { includeConfig 'conf/test_minimal.config'              }
    test_multi_sample_with_gz { includeConfig 'conf/test_multi_sample_with_gz.config' }
    test_merge                { includeConfig 'conf/test_merge.config'                }
    test_update               { includeConfig 'conf/test_update.config'               }
    test_full                 { includeConfig 'conf/test_full.config'                 }
}

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/proteinfamilies 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"


// Load nf-core/proteinfamilies custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinfamilies.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/proteinfamilies'
    contributors    = [
        [
            name: 'Evangelos Karatzas',
            affiliation: 'EMBL-EBI',
            email: 'vangelis@ebi.ac.uk',
            github: 'https://github.com/vagkaratzas',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-9132-8981'
        ],
        [
            name: 'Martin Beracochea',
            affiliation: 'EMBL-EBI',
            github: 'https://github.com/mberacochea',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0003-3472-3736'
        ]
    ]
    homePage        = 'https://github.com/nf-core/proteinfamilies'
    description     = """Generate protein family level models (Multiple Sequence Alignments (MSAs), Hidden Markov Models (HMMs)) starting from a FASTA amino acid sequence file."""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=25.10.0'
    version         = '2.1.0'
    doi             = '10.1101/2025.08.12.670010, 10.5281/zenodo.14881993'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

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

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