nf-configs/conf/pipeline/eager/eva.config

// Profile config names for nf-core/configs

params {
  // Specific nf-core/configs params
  config_profile_contact = 'James Fellows Yates (@jfy133)'
  config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
}

// Specific nf-core/eager process configuration
process {

  beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'

  maxRetries = 2

  // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
  clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }

  withLabel:'sc_tiny'{
    cpus = { check_max( 1, 'cpus' ) }
    memory = { check_max( 1.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'sc_small'{
    cpus = { check_max( 1, 'cpus' ) }
    memory = { check_max( 4.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'sc_medium'{
    cpus = { check_max( 1, 'cpus' ) }
    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'mc_small'{
    cpus = { check_max( 2, 'cpus' ) }
    memory = { check_max( 4.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'mc_medium' {
    cpus = { check_max( 4, 'cpus' ) }
    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'mc_large'{
     cpus = { check_max( 8, 'cpus' ) }
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    time = '365.d'
  }

  withLabel:'mc_huge'{
     cpus = { check_max( 32, 'cpus' ) }
     memory = { check_max( 256.GB * task.attempt, 'memory' ) }
    time = '365.d'
   }
  
  // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use

  withName: makeSeqDict {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }
      
  withName: fastqc {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: adapter_removal {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }
   
  withName: bwa {
    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
  }
  
  withName: bwamem {
    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
  }
  
  withName: circularmapper {
    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
  }
  
  withName: bowtie2 {
    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
  }

  withName: samtools_flagstat {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
  }
  
  withName: samtools_flagstat_after_filter {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
  }

  withName: dedup {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: markduplicates {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    memory = { check_max( 20.GB * task.attempt, 'memory' ) }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }
   
  withName: library_merge {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
   }

  withName: seqtype_merge {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
   }
   
   withName: additional_library_merge {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    memory = { check_max( 4.GB * task.attempt, 'memory' ) }
   }
   
   withName: metagenomic_complexity_filter {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
   }

  withName: malt {
    clusterOptions = { "-V -l h_vmem=1000G" }
    cpus = { check_max( 32, 'cpus' ) }
    memory = { check_max( 955.GB * task.attempt, 'memory' ) }
   }

  withName: maltextract {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: multivcfanalyzer {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: mtnucratio {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: vcf2genome {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: qualimap {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
   }

  withName: damageprofiler {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: circularmapper {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: circulargenerator {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

  withName: preseq {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
   }
   
  withName: genotyping_ug {
    clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
   }

}

profiles {
 
  medium_data {
  
    params {
      // Specific nf-core/configs params
      config_profile_contact = 'James Fellows Yates (@jfy133)'
      config_profile_description = 'nf-core/eager medium-data EVA profile provided by nf-core/configs'
    }
  
    executor {
      queueSize = 8
     }

    process {

        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'

        maxRetries = 2

        // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
        clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }

        withLabel:'sc_tiny'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
        }

        withLabel:'sc_small'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 6.GB * task.attempt, 'memory' ) }
        }

        withLabel:'sc_medium'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 12.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_small'{
          cpus = { check_max( 2, 'cpus' ) }
          memory = { check_max( 6.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_medium' {
          cpus = { check_max( 4, 'cpus' ) }
          memory = { check_max( 12.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_large'{
          cpus = { check_max( 8, 'cpus' ) }
          memory = { check_max( 24.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_huge'{
          cpus = { check_max( 32, 'cpus' ) }
          memory = { check_max( 256.GB * task.attempt, 'memory' ) }
        }

        // Fixes for SGE and Java incompatibility due to  (and also some samtools?!) using more memory than you tell it to use

        withName: makeSeqDict {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
            
        withName: fastqc {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: adapter_removal {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: samtools_flagstat {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
        }
        
        withName: samtools_flagstat_after_filter {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
        }

        withName: dedup {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: markduplicates {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          memory = { check_max( 32.GB * task.attempt, 'memory' ) }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
        
        withName: library_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
         }

        withName: seqtype_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
         }

         withName: additional_library_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          memory = { check_max( 4.GB * task.attempt, 'memory' ) }
         }

        withName: metagenomic_complexity_filter {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
        }

        withName: malt {
          clusterOptions = { "-V -l h_vmem=1000G" }
          cpus = { check_max( 32, 'cpus' ) }
          memory = { check_max( 955.GB * task.attempt, 'memory' ) }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }

        withName:hostremoval_input_fastq {
          memory = { check_max( 32.GB * task.attempt, 'memory' ) }
        }

        withName: maltextract {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: multivcfanalyzer {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: mtnucratio {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: vcf2genome {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: qualimap {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
        }

        withName: damageprofiler {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          memory = { check_max( 16.GB * task.attempt, 'memory' ) }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: circularmapper {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: circulargenerator {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
        
        withName: genotyping_ug {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: preseq {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
          errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
        }

      }
  }

  big_data {
  
    params {
      // Specific nf-core/configs params
      config_profile_contact = 'James Fellows Yates (@jfy133)'
      config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
    }
  
    executor {
      queueSize = 6
     }

    process {

        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'

        maxRetries = 2

        // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
        clusterOptions = { "-V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }

        withLabel:'sc_tiny'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 2.GB * task.attempt, 'memory' ) }
        }

        withLabel:'sc_small'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 8.GB * task.attempt, 'memory' ) }
        }

        withLabel:'sc_medium'{
          cpus = { check_max( 1, 'cpus' ) }
          memory = { check_max( 16.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_small'{
          cpus = { check_max( 2, 'cpus' ) }
          memory = { check_max( 8.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_medium' {
          cpus = { check_max( 4, 'cpus' ) }
          memory = { check_max( 16.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_large'{
           cpus = { check_max( 8, 'cpus' ) }
           memory = { check_max( 32.GB * task.attempt, 'memory' ) }
        }

        withLabel:'mc_huge'{
           cpus = { check_max( 32, 'cpus' ) }
           memory = { check_max( 512.GB * task.attempt, 'memory' ) }
         }

        // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use

        withName: makeSeqDict {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
            
        withName: fastqc {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: adapter_removal {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: samtools_flagstat {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
        }
        
        withName: samtools_flagstat_after_filter {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
        }

        withName: dedup {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: markduplicates {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          memory = { check_max( 48.GB * task.attempt, 'memory' ) }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
        
        withName: library_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          memory = { check_max( 6.GB * task.attempt, 'memory' ) }
         }

        withName: seqtype_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
         }

         withName: additional_library_merge {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          memory = { check_max( 6.GB * task.attempt, 'memory' ) }
         }

        withName:hostremoval_input_fastq {
          memory = { check_max( 32.GB * task.attempt, 'memory' ) }
        }

        withName: metagenomic_complexity_filter {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
        }

        withName: malt {
          clusterOptions = { "-V -l h_vmem=1000G" }
          cpus = { check_max( 32, 'cpus' ) }
          memory = { check_max( 955.GB * task.attempt, 'memory' ) }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }

        withName: maltextract {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: multivcfanalyzer {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: mtnucratio {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: vcf2genome {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: qualimap {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
        }

        withName: damageprofiler {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          memory = { check_max( 32.GB * task.attempt, 'memory' ) }         
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: circularmapper {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }

        withName: circulargenerator {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
        
        withName: genotyping_ug {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
        }
        
        withName: preseq {
          clusterOptions = { "-V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
          errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
        }

      }
  }
  
  pathogen_loose {
    params {
      config_profile_description = 'Pathogen (loose) MPI-EVA profile, provided by nf-core/configs.'
      bwaalnn = 0.01
      bwaalnl = 16
    }
  }
  pathogen_strict {
    params {
      config_profile_description = 'Pathogen (strict) MPI-EVA SDAG profile, provided by nf-core/configs.'
      bwaalnn = 0.1
      bwaalnl = 32
     }
  }
  human {
      params {
      config_profile_description = 'Human MPI-EVA SDAG profile, provided by nf-core/configs.'
      bwaalnn = 0.01
      bwaalnl = 16500
     }
  }
}