/*
 * -------------------------------------------------
 *  Nextflow config file for running nf-core eager on whole genome data or mitogenomes 
 * -------------------------------------------------
 * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
 */

params {

   config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'

   config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "

}


profiles {

   nuclear {
      process {
         errorStrategy = 'retry'
         maxRetries = 2

         withName:'makeBWAIndex'{
            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 12.h * task.attempt, 'time' ) }
         }
         withName:'adapter_removal'{
            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
            time = { check_max( 12.h * task.attempt, 'time' ) }
         }
         withName:'bwa'{
            cpus = { check_max( 40 * task.attempt, 'cpus' ) }
            memory = { check_max( 40.GB * task.attempt, 'memory' ) }
            time = 24.h 
            cache = 'deep'
         }
         withName:'markduplicates'{
            errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
            cpus = { check_max( 16 * task.attempt, 'cpus' ) }
            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
            time = { check_max( 12.h * task.attempt, 'time' ) }
         }
         withName:'damageprofiler'{
            cpus = 1
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 6.h * task.attempt, 'time' ) }
         }
         withName:'fastp'{
            cpus = 8 
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 6.h * task.attempt, 'time' ) }
         }
         withName:'fastqc'{
            cpus = 2
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 6.h * task.attempt, 'time' ) }
         }
      }
   }

   mitocondrial {
      process {
         errorStrategy = 'retry'
         maxRetries = 2

         withName:'makeBWAIndex'{
            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 12.h * task.attempt, 'time' ) }
         }
         withName:'adapter_removal'{
            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
            time = { check_max( 12.h * task.attempt, 'time' ) }
         }
         withName:'bwa'{
            cpus = { check_max( 5 * task.attempt, 'cpus' ) }
            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
            time = 24.h 
         }
         withName:'markduplicates'{
            errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
            cpus = { check_max( 5 * task.attempt, 'cpus' ) }
            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
            time = { check_max( 6.h * task.attempt, 'time' ) }
         }
         withName:'damageprofiler'{
            cpus = 1
            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
            time = { check_max( 3.h * task.attempt, 'time' ) }
         }
         withName:'fastp'{
            cpus = 8 
            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
            time = { check_max( 3.h * task.attempt, 'time' ) }
         }
         withName:'fastqc'{
            cpus = 2
            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
            time = { check_max( 6.h * task.attempt, 'time' ) }
         }
      }
   }
   unlimitedtime {
     process {
        errorStrategy = 'finish'

        cpus = 5
        memory = 200.GB
        time = 8760.h

    }
}