nextflow.config

/*
========================================================================================
    Input Parameters
========================================================================================
*/

params {
  input_data = "nb_CD14_Mono_Memory_data.yaml"

  // Assays to run, options are: RNA, ATAC, HiC, Multiome
  assays = ['ATAC']

  // Components to run, options are: dim_reduct, clustering, batch_correction, scalability.
  // If unspecified, all components will be run.
  //components = ['batch_correction', 'dim_reduct']
  components = null

  // Output options
  outdir = "results"

  // Available methods, options are: pca, snapatac2, snapatac, signac, archr, 
  // peakvi, scale, scbasset, cistopic
  // If unspecified, all methods will be run.
  //method_include = ['pca', 'snapatac2', 'snapatac', 'signac', 'archr', 'scale', 'peakvi', 'cistopic', 'scbasset']
  method_include = null
  method_exclude = null


  
}

/*
========================================================================================
    Nextflow Metrics & Reports
========================================================================================
*/

timeline {
  enabled = true
  file    = "${params.outdir}/timeline.html"
}

report {
  enabled = true
  file    = "${params.outdir}/report.html"
}
trace {
  enabled = true
  overwrite = true
  fields  = 'task_id,hash,name,status,exit,realtime,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar'
  file    = "${params.outdir}/trace.txt"
}

/*
========================================================================================
    Profiles - slurm,singularity,conda,docker
========================================================================================
*/


profiles {
  glean {
    executor {
      name='pbs'
      queueSize=50
    }
    process {
      executor = 'pbs'
      clusterOptions = "-q glean -l walltime=8:00:00 -l nodes=1:ppn=8"

      withLabel: gpu {
        clusterOptions = "-q glean -l walltime=8:00:00 -l nodes=1:ppn=4:A100"
      }
    }
  }

  home {
    executor {
      name='pbs'
      queueSize=50
    }
    process {
      executor = 'pbs'
      clusterOptions = "-q home-ren -l walltime=48:00:00"

      withLabel: gpu {
        clusterOptions = "-q gpu-hotel -l walltime=24:00:00 -l nodes=1:ppn=4:A100"
      }
    }
  }

  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
  
  docker {
    docker.enabled = true
  }
}