nf-configs/conf/pipeline/viralrecon/eddie.config

env {
  BLASTDB_LMDB_MAP_SIZE=100000000
}

process {
  withName : '.*PICARD.*' {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }

  withName : '.*SNPEFF.*' {
    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
  }
}
Set BLASTDB_LMDB_MAP_SIZE This environment variable needs to be set in order to prevent memory allocation errors in the MAKEBLASTDB process. 2021-07-22 14:07:19 +00:00			`env {`
			`BLASTDB_LMDB_MAP_SIZE=100000000`
			`}`

eddie.config for viralrecon pipeline 2021-07-21 11:10:43 +00:00			`process {`
			`withName : '.PICARD.' {`
			`clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}`
			`}`

			`withName : '.SNPEFF.' {`
			`clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}`
			`}`
			`}`