/*
 * -------------------------------------------------
 *  Nextflow config file for running tests
 * -------------------------------------------------
 * Defines bundled input files and everything required
 * to run a fast and simple test. Use as follows:
 *   nextflow run nf-core/coproid -profile test,<docker/singularity>
 */

params {
  config_profile_name = 'Test profile'
  config_profile_description = 'Minimal test dataset to check pipeline function'
  // Limit resources so that this can run on GitHub Actions
  max_cpus = 2
  max_memory = 6.GB
  max_time = 48.h

  // Input data
  single_end = false
  readPaths = [
    ['metagenome',
      [
        "https://github.com/nf-core/test-datasets/raw/coproid/reads/metagenome.1.fastq.gz",
        "https://github.com/nf-core/test-datasets/raw/coproid/reads/metagenome.2.fastq.gz"
      ]
    ],
    ['metagenomebis',
      [
        "https://github.com/nf-core/test-datasets/raw/coproid/reads/metagenomebis.1.fastq.gz",
        "https://github.com/nf-core/test-datasets/raw/coproid/reads/metagenomebis.2.fastq.gz"
      ]
    ]
  ]
  fasta1 = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/ecoli/genome.fa"
  fasta2 = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/bsubtilis/genome.fa"
  name1 = "Bacillus_subtilis"
  name2 = "Escherichia_coli"
  // index1 = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/bsubtilis/Bowtie2Index.tar.gz"
  // index2 = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/genomes/ecoli/Bowtie2Index.tar.gz"
  krakendb = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/kraken.tar.gz"
  phred = 64
  genome1 = ""
  genome2 = ""
  sp_sources = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/sourcepredict/test_sources.csv"
  sp_labels = "https://raw.githubusercontent.com/nf-core/test-datasets/coproid/sourcepredict/test_labels.csv"
  sp_norm = 'subsample'
  sp_embed = 'tsne'
  sp_neighbors = '0'
}

process {
  stageInMode = "copy"
  stageOutMode = "copy"
}
