profiles {
  standard {
    includeConfig 'configs/biohpc.config'
  }
  biohpc_local {
    includeConfig 'configs/biohpc_local.config'
  }
  aws_ondemand {
    includeConfig 'configs/aws_ondemand.config'
  }
  aws_spot {
    includeConfig 'configs/aws_spot.config'
  }
}

trace {
  enabled = true
  file = 'pipeline_trace.txt'
  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
}

timeline {
  enabled = true
  file = 'timeline.html'
}
	
report {
  enabled = true
  file = 'report.html'
}

tower {
  enabled = true
  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
}

manifest {
  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcl's and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
  mainScript = 'main.nf'
  version = '2.0.0-indev'
  nextflowVersion = '>=0.31.0'
}