nextflow.config

profiles {

   standard {
      includeConfig 'base.config'
      process.executor = 'local'
      conda.enabled = true
      process {
         withName: 'PORECHOP|FILTLONG' {
               conda = "${baseDir}/Docker/conda_environments/porechop_filtlong.yml"
         }
         withName: NANOPLOT{
               conda = "${baseDir}/Docker/conda_environments/nanoplot.yml"
         }
	 withName: GENOME_SIZE_ESTIMATION{
               conda = "${baseDir}/Docker/conda_environments/kat.yml"
         }
         withName: FLYE{
               conda = "${baseDir}/Docker/conda_environments/flye.yml"
         }
         withName: 'MEDAKA_FIRST_ITERATION|MEDAKA_SECOND_ITERATION' {
               conda = "${baseDir}/Docker/conda_environments/medaka.yml"
         }
         withName: 'QUAST|QUAST_MULTIQC' {
               conda = "${baseDir}/Docker/conda_environments/quast.yml"
         }
      }
   }

   docker {
      includeConfig 'base.config'
      process.executor = 'local'
      process.container = 'erkison/long_read_assembly:0.1'
      docker.enabled = true
      docker.runOptions='-u $(id -u):$(id -g)'
      errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
      maxRetries = 5 
   }

}