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

params {
  config_profile_name = 'Full test profile for nf-core/eager'
  config_profile_description = 'Full test dataset to check nf-core/eager function'

  // Input data for full size test
  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Benchmarking/benchmarking_vikingfish.tsv'
   
   // Genome reference
   fasta = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Gadus_morhua/representative/GCF_902167405.1_gadMor3.0/GCF_902167405.1_gadMor3.0_genomic.fna.gz'
   
   bwaalnn = 0.04
   bwaalnl = 1024
   
   run_bam_filtering = true
   bam_discard_unmapped = true
   bam_unmapped_type = 'discard'
   bam_mapping_quality_threshold = 25
     
   run_genotyping = true
   genotyping_tool = 'hc'
   genotyping_source = 'raw'
   gatk_ploidy = 2
}

process {
   withName:'adapter_removal'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withName:'bwa'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 8.h * task.attempt, 'time' ) }
   }
   withName:'dedup'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 4.h * task.attempt, 'time' ) }
   }
   withName:'genotyping_hc'{
     cpus = { check_max( 8, 'cpus' ) }
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
     time = { check_max( 8.h * task.attempt, 'time' ) }
   }
   
  // Ignore `--input` as otherwise the parameter validation will throw an error
  schema_ignore_params = 'genomes,input_paths,input'
}
