/*
 * -------------------------------------------------
 *  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/sarek -profile test,<docker/singularity>
 */

params {
  config_profile_description = 'Minimal test dataset to check pipeline function'
  config_profile_name = 'Test profile'

  // Limit resources so that this can run on GitHub Actions
  max_cpus = 2
  max_memory = 6.GB
  max_time = 48.h

  // Input data
  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv'

  // Small reference genome
  igenomes_ignore = true
  genome = 'smallGRCh37'
  genomes_base = "https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference"
  snpeff_db         = 'WBcel235.86'
  species           = 'caenorhabditis_elegans'
  vep_cache_version = '99'

  // Ignore `--input` as otherwise the parameter validation will throw an error
  schema_ignore_params = 'genomes,input'
}

process {
  withName:Snpeff {
    container = 'nfcore/sareksnpeff:2.7.2.WBcel235'
    maxForks = 1
  }
  withLabel:VEP {
    container = 'nfcore/sarekvep:2.7.2.WBcel235'
    maxForks = 1
  }
}
