SciLifeLab / NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
https://ngisweden.scilifelab.se/
MIT License
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Memory requirement for local jobs too high #192

Closed orzechoj closed 6 years ago

orzechoj commented 6 years ago

The jobs run locally (i.e. on the login node) are get_software_versions and multiqc. These fail when I run them on bianca, where I can only get 7Gb memory on the login node. Currently I use the pipeline with base config file like this:

  $multiqc {
    memory = { check_max( 2.GB * task.attempt, 'memory' ) }
    executor = 'local'
    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  }
  $get_software_versions {
    memory = { check_max( 2.GB * task.attempt, 'memory' ) }
    executor = 'local'
    errorStrategy = 'ignore'
  }