nextflow.config

params {
    
    // input data
    count             = "${baseDir}/data/genes770/count.csv.gz"
    
    // output
    outdir            = "${baseDir}/results"
    tracedir          = "${params.outdir}/pipeline_info"

    // parameters
    imputation        = ['CZM'] // ['CZM','GBM','lrSVD','freqshrink']
    transformation    = ['clr'] // ['alr','clr']
    ncell             = [100] // [100,1000,2500]
    ngene             = [200]
    nsamp             = 200

    // r helper functions
    rlib              = "${baseDir}/bin/rlib"

}


// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
includeConfig 'conf/params.config'

profiles {
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled              = false
    singularity.enabled         = false
    podman.enabled              = false
    shifter.enabled             = false
    charliecloud.enabled        = false
    // Avoid this error:
    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
    // once this is established and works well, nextflow might implement this behavior as new default.
    docker.runOptions = '-u \$(id -u):\$(id -g)'
  }
  singularity {
    singularity.enabled         = true
    singularity.autoMounts      = true
    docker.enabled              = false
    podman.enabled              = false
    shifter.enabled             = false
    charliecloud.enabled        = false
  }
  crg   { includeConfig 'conf/crg.config'   }
  trace { includeConfig 'conf/trace.config' }
}