nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    UPHL-BioNGS/Grandeur Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Nextflow plugins
plugins {
    id 'nf-schema@2.5.1'
}

params {
  outdir = "grandeur"

  // Input options
  reads                = null
  fastas               = null
  input                = null
  sample_sheet         = params.input
  fasta_list           = null

  // external files
  kraken2_db           = null
  checkm2_db           = null
  mash_db              = null
  sylph_db             = null
  reference_genomes    = null

  // for downloading from databases
  sra_accessions       = null
  genome_accessions    = null

  // thresholds and other params
  minimum_reads        = 10000
  min_core_genes       = 500
  min_core_per         = 0.5

  // subworkflow flags
  current_datasets     = false
  skip_extras          = false
  exclude_top_hit      = false
  msa                  = false

  // specifying the core workflow
  aligner              = 'panaroo'
  annotator            = 'bakta'

  // for qc
  genome_sizes         = null

  // for portability
  container_registry   = 'docker.io'

  // the following were stolen from other nf-core workflows and may have no functionality here

  // Boilerplate options
  trace_report_suffix          = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
  publish_dir_mode             = 'copy'
  email                        = null
  email_on_fail                = null
  plaintext_email              = false
  monochrome_logs              = false
  hook_url                     = null
  help                         = false
  version                      = false
  pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'

  // 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
  help                       = false
  help_full                  = false
  show_hidden                = false
}


// 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" 


//########## Setting Profiles ##########

profiles {
  apptainer {
        apptainer.enabled      = true
        apptainer.autoMounts   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
        shifter.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)'
    }
  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
    }
  msa {
    params.msa                    = true
    }
  just_msa {
    params.msa                    = true
    params.skip_extras            = true
    }
  test {
    // default workflow
    params.sra_accessions         = ["SRR11725329", "SRR13643280", "SRR14436834", "SRR14634837", "SRR7738178", "SRR7889058"]
    }
  test_full {
    params.sample_sheet           = "${projectDir}/tests/sample_sheet.csv"
  }
  test0 {
    // default workflow while skipping extras
    params.sra_accessions         = ["SRR11725329", "SRR13643280"]
    params.skip_extras            = true
    }
  test1 {
    // turning on current datasets
    params.sra_accessions         = ["SRR11725329", "SRR13643280", "SRR14436834", "SRR14634837", "SRR7738178", "SRR7889058"]
    params.current_datasets       = true
    }
  test2 {
    // phylogenetic analysis
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    }
  test3 {
    // phylogenetic analysis without extras
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    params.skip_extras            = true
    }
  test4 {
    // phylogenetic analysis with current datasets
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    params.current_datasets       = true
    }
  test5 {
    // phylogenetic analysis and ani top hit
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    params.exclude_top_hit        = true
    }
  test6 {
    // phylogenetic analysis with roary and exclude ani top hit
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    params.exclude_top_hit        = true
    params.aligner                = 'roary'
    }
  uphl {
    includeConfig './conf/UPHL.config'
    }
  healthomics {
    includeConfig './conf/healthomics.config'
  }
  slurm {
    includeConfig './conf/slurm.config'
    }
  test7 {
    // phylogenetic analysis with prokka and exclude ani top hit
    params.sra_accessions         = ["SRR22314961", "SRR22314960", "SRR22314959", "SRR22314958" ]
    params.msa                    = true
    params.annotator              = 'prokka'
    }
  test8 {
    // phylogenetic analysis with genome accessions
    params.genome_accessions      = ["GCF_900475035.1", "GCF_022869605.1", "GCF_002055535.1", "GCF_004028355.1" ]
    params.msa                    = true
    }

}

nextflow.enable.configProcessNamesValidation = false

// Set all container engines to default to Docker Hub
docker.registry       = "${params.container_registry}"
podman.registry       = "${params.container_registry}"
singularity.registry  = "${params.container_registry}"
apptainer.registry    = "${params.container_registry}"
charliecloud.registry = "${params.container_registry}"

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                            = 'UPHL-BioNGS/Grandeur'
  author                          = 'Erin Young'
  homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
  mainScript                      = 'main.nf'
  version                         = '5.1.26218'
  defaultBranch                   = 'main'
  description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
  nextflowVersion                 = '!>=25.0.0'
}


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

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