nextflow.config

profiles {
  core {
    params {
      proteomes = "$baseDir/data/core/test.tar.gz"
      outputDir = "$launchDir/coreOutput"
      outdatedOrganisms = "$baseDir/data/core/outdated.txt"
      diamondSimilarityCache = "$baseDir/data/core/diamondSimilarityCache"
      orthoFinderDiamondOutputFields = "qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
      buildVersion = "7"
    }
    docker {
      enabled = true
      runOptions='--user root'
    }
    singularity {
      enabled = false
    }
  }
  peripheral {
    params {
      outputDir = "$launchDir/output"
      coreProteomes = "$baseDir/data/core/test.tar.gz"
      peripheralProteomes = "$baseDir/data/peripherals/peripherals.tar.gz"
      coreGroupsFile = "$baseDir/coreOutput/reformattedGroups.txt"
      coreGroupSimilarities = "$baseDir/coreOutput/groupDiamondResults"
      coreTranslateSequenceFile = "$baseDir/coreOutput/diamondCache/SequenceIDs.txt"
      outdatedOrganisms = "$baseDir/data/peripherals/outdated.txt"
      peripheralDiamondCache = "$baseDir/data/peripherals/cache"
      outputDir = "$launchDir/peripheralOutput"
      buildVersion = "7"
      orthoFinderDiamondOutputFields = "qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
      bestRepDiamondOutputFields = "qseqid sseqid evalue"      
    }
    docker {
      enabled = true
    }
    singularity {
      enabled = false
    }

  }
}