// Profile config names for nf-core/configs

params {
  // Specific nf-core/configs params
  config_profile_contact = 'James Fellows Yates (@jfy133)'
  config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
  igenomes_base = "/projects1/public_data/igenomes/"
}

// Specific nf-core/eager process configuration
process {

  maxRetries = 5

  withName: malt {
    maxRetries = 1
    memory = {  task.attempt > 1 ? 1900.GB : 725.GB }
    cpus = { task.attempt > 1 ? 112 : 64 }
    time = 1440.h
    queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
  }
}

profiles {
  hops {
    pathogen_screening {
      fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
      bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
      fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
      seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
      bwaalnn = 0.04
      bwaalnl = 32
      run_bam_filtering = true
      bam_discard_unmapped = true
      bam_unmapped_type = 'fastq'
      run_metagenomic_screening = true
      metagenomic_tool = 'malt'
      metagenomic_min_support_reads = 1
      database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017'
      percent_identity = 90
      malt_mode = 'BlastN'
      malt_alignment_mode = 'SemiGlobal'
      malt_top_percent = 1
      malt_min_support_mode = 'percent'
      malt_min_support_percent = 0.01
      malt_max_queries = 100
      malt_memory_mode = 'load'
      run_maltextract = true
      maltextract_taxon_list = '/projects1/users/key/anc5h/soi.backup/List_of_pathogens_KB_fmk12_wViruses1.txt'
      maltextract_ncbifiles = '/projects1/clusterhomes/huebler/RMASifter/RMA_Extractor_Resources/'
      maltextract_filter = 'def_anc'
      maltextract_toppercent = 0.01
      maltextract_destackingoff = false
      maltextract_downsamplingoff = false
      maltextract_duplicateremovaloff = false
      maltextract_matches = false
      maltextract_megansummary = false
      maltextract_percentidentity = 90.0
      maltextract_topalignment =  false
      maltextract_singlestranded = false
    }
  }
  pathogen_loose {
    params {
      config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'
      bwaalnn = 0.01
      bwaalnl = 16
    }
  }
  pathogen_strict {
    params {
      config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.'
      bwaalnn = 0.1
      bwaalnl = 32
     }
  }
  human {
      params {
      config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.'
      bwaalnn = 0.01
      bwaalnl = 16500
     }
  }
}