MUNIN Configuration

All nf-core pipelines have been successfully configured for use on the MUNIN cluster.

Usage

To use, run the pipeline with -profile munin.

This will download and launch the munin.config which has been pre-configured with a setup suitable for the MUNIN cluster.

Example: nextflow run -profile munin

Singularity

This is the default behavior of this configuration profile.

Using this profile, if no singularity image are available, one will be downloaded from dockerhub, and converted to a Singularity image before execution of the pipeline.

It is also possible to specify the singularity profile:

Example: nextflow run -profile munin,singularity

Docker

It is also possible to execute the pipeline using Docker.

Using this profile, if no docker image are available, one will be downloaded from dockerhub before execution of the pipeline.

Example: nextflow run -profile munin,docker

Below are non-mandatory information on iGenomes specific configuration

A local copy of the iGenomes resource has been made available on the MUNIN cluster so you should be able to run the pipeline against any reference available in the igenomes.config specific to the nf-core pipeline. You can do this by simply using the --genome <GENOME_ID> parameter.

NB: You will need an account to use the MUNIN cluster in order to run the pipeline. If in doubt contact @szilva.

Config file

See config file on GitHub

munin.config
// Profile config names for nf-core/configs
 
params {
  // Specific nf-core/configs params
  config_profile_contact = 'Maxime Garcia (@maxulysse)'
  config_profile_description = 'MUNIN profile provided by nf-core/configs'
  config_profile_url = 'https://ki.se/forskning/barntumorbanken'
 
  // Local AWS iGenomes reference file paths on munin
  igenomes_base = '/data1/references/igenomes/'
 
  // General cpus/memory/time requirements
  max_cpus = 46
  max_memory = 752.GB
  max_time = 72.h
}
 
process {
  executor = 'local'
  maxForks = 46
 
// Limit cpus for Mutect2
  withName:'Mutect2|Mutect2Single|PileupSummariesForMutect2' {
    time = {48.h * task.attempt}
    maxForks = 12
  }
}
 
singularity {
  cacheDir   = '/data1/containers/'
  enabled    = true
  //runOptions = "--bind /media/BTB_2021_01"
}
 
// To use docker, use nextflow run -profile munin,docker
profiles {
  docker {
    docker {
      enabled = false
      mountFlags = 'z'
      fixOwnership = true
    }
  }
}