nextflow.config

#! /usr/bin/env nextflow

// default params, explained in main.nf --help
params.help = false

// input images are listed in this file, one image per line
params.image_file = "images.txt"

//
// pre-processing
//

// psf matching via convolution
params.convolve = false

// fits/flux warping
params.fits_warp = false
params.ref_catalogue = null
params.refcat_ra = 'RAJ2000'
params.refcat_dec = 'DEJ2000'

params.flux_warp = false

// monitoring of a pre-determined source
params.use_monitoring_src_file = false
params.monitoring_src_file = ""

// Source finding region file
params.use_region_file = false
params.region_file = ""

// calling stilts
params.stilts = "stilts"

// calling swarp
params.swarp = "SWarp"

// Source finding params
params.region_file = "square.mim"

// Plotting options
params.plotdates = true

// output directory
params.output_dir = 'results/'
params.keep_epoch_images = false

// turn on all the juicy logging
trace.enabled = true
timeline.enabled = true
report.enabled = true
dag.enabled = true

// get hostname
host = 'none' //"$HOSTNAME".split('-')[0]

profiles {
    local {
      executor {
        name = 'local'
        queueSize = 1
        cpus = 6
        memory = 24G
      }
      process {
        container = 'paulhancock/robbie-next:latest'
        publishDir = [path:params.output_dir, mode:'copy', overwite:true]
      }
      // params.stilts = "java -jar /home/paulhancock/Software/topcat/topcat-full.jar -stilts"
      docker {
        enabled = true
        temp = 'auto'
        runOptions = '--user "$(id -u):$(id -g)"'
      }
    }
    hpc {
      singularity {
        enabled = true
        autoMounts = true
        cacheDir = '/group/mwasci/phancock/.singularity'
        runOptions = '-B /pawsey'
      }
      executor {
        name = 'slurm'
        clusterOptions = '--account=pawsey0345'
        submitRateLimit = '10 sec'
        queueSize = 96
        account = 'pawsey0345'
      }

      process {
       publishDir = [path:params.output_dir, mode:'link', overwite:true]
      }

    }

    zeus {
      process {
        executor = 'slurm'
        queue = 'workq'
        cpus = 28
        memory = '60 GB'
        time = '1 h'
        container = 'paulhancock/robbie-next'
      }
    }

    magnus {
      process{
        executor = 'slurm'
        queue = 'workq'
        cpus = 24
        memory = '60 GB'
        time = '1 h'
        container = 'paulhancock/robbie-next'
      }
    }
}

if ( host == "garrawarla") {
  // Set up container
  process.module = 'singularity/3.7.4'
  singularity {
    enabled = true
    envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH'
    runOptions = '--bind $HOME:/$HOME'
  }
  params.containerDir = '/pawsey/mwa/singularity'

  executor {
    name = 'slurm'
    submitRateLimit = '10 sec'
    queueSize = 96
    //envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH'
  }
  process {
    // TODO change this to the "latest" sim link once testing is complete
    container = "file:///${params.containerDir}/robbie/robbie-next_2.2.1.sif"
    queue = 'workq'
    cpus = 28
    memory = '60 GB'
    time = '1 h'
  }



}