nextflow.config

params {
  
  protocol_template_dir = "${baseDir}/assets/protocols"
  instructions_dir = "${baseDir}/assets/instructions"
  opentrons_labware_dir = "${baseDir}/assets/labware"
  resultsDir = "./results/"

  // PROTOCOL 1 SETTINGS
  protocol_1_config = "${baseDir}/assets/testdata/protocol-1-config.json"
  protocol_1_data = "${baseDir}/assets/testdata/protocol-1-data.csv"
  protocol_1_instructions = "${baseDir}/assets/instructions/protocol-1-instructions.Rmd"

  // PROTOCOL 2 SETTINGS
  protocol_2_config = "${baseDir}/assets/testdata/protocol-2-config.json"
  protocol_2_data = "${baseDir}/assets/testdata/protocol-2-data.csv"
  protocol_2_instructions = "${baseDir}/assets/instructions/protocol-2-instructions.Rmd"

  // PROTOCOL 3 SETTINGS
  protocol_3_config = "${baseDir}/assets/testdata/protocol-3-config.json"
  protocol_3_data = "${baseDir}/assets/testdata/protocol-3-data.csv"
  protocol_3_instructions = "${baseDir}/assets/instructions/protocol-3-instructions.Rmd"

  // PROTOCOL 4 SETTINGS
  protocol_4_config = "${baseDir}/assets/testdata/protocol-4-config.json"
  protocol_4_data = "${baseDir}/assets/testdata/protocol-4-data.csv"
  protocol_4_instructions = "${baseDir}/assets/instructions/protocol-4-instructions.Rmd"

  // PROTOCOL 5 SETTINGS
  protocol_5_config = "${baseDir}/assets/testdata/protocol-5-config.json"
  protocol_5_data = "${baseDir}/assets/testdata/protocol-5-data.csv"
  protocol_5_instructions = "${baseDir}/assets/instructions/protocol-5-instructions.Rmd"

  // PROTOCOL 6 SETTINGS
  protocol_6_config = "${baseDir}/assets/testdata/protocol-6-config.json"
  protocol_6_data = "${baseDir}/assets/testdata/protocol-6-data.csv"
  protocol_6_instructions = "${baseDir}/assets/instructions/protocol-6-instructions.Rmd"

  // PROTOCOL 7 SETTINGS
  protocol_7_config = "${baseDir}/assets/testdata/protocol-7-config.json"
  protocol_7_data = "${baseDir}/assets/testdata/protocol-7-data.csv"
  protocol_7_instructions = "${baseDir}/assets/instructions/protocol-7-instructions.Rmd"

}

includeConfig 'conf/base.config'