Configuration

MIAAIM utilizes software containers for individual processes within its Nextflow workflow. Configuration settings for each individual process can be set using the nextflow.config file in the main MIAAIM repository. Passing configuration settings to Nextflow upon running your analysis is done by specifying your

Docker/Singularity Containers

Resource Allocation

Configuring resource allocation within each Docker image can be achieved by modifying or adding configuration files (in config folder of MIAAIM repo) and linking those with the nextflow.config file in the main repository.

miaaim                    # main repository
├── LICENSE
├── README.md
├── miaam.nf
├── nextflow.config       # Nextflow configuration in main repo
├── workflows
├── docs
├── config                # config folder with custom configurations
│   └──medium.config      # example configuration file that can be modified or added

Each of your processes within the MIAAIM pipeline can have resources allocated to its respective container image.

Memory

Memory allocation can be set for individual processes using the memory indicator. For example, this is the medium.config file for jobs that require medium sized memory allocation. This file sets a time limit on each process, and allocates 40GB of memory to each.

process {
  withName:hdiprep   {
    time   = '6h'
    memory = '40G'
  }
  withName:elastix   {
    time   = '6h'
    memory = '40G'
  }
  withName:transformix   {
    time   = '6h'
    memory = '40G'
  }
}

CPU

CPU allocation can be set for individual processes using the cpu indicator. For example, this is the multi.config file for jobs that require multiple cpus. This file sets a time limit on each process, and allocates 30 cpus to each.

process {
  withName:hdiprep   {
    time   = '6h'
    cpus = 30
  }
  withName:elastix   {
    time   = '6h'
    cpus = 30
  }
  withName:transformix   {
    time   = '6h'
    cpus = 30
  }
}

Preset Resource Allocation Options

MIAAIM provides sensible defaults for job scheduling. We separated cpu usage from memory allocation to provide a mix of resource usage options. Feel free to add or modify our configuration settings within your project!

Preset Resource Allocation Options in MIAAIM

Flag	Memory	CPUs
medium	40GB
multi		30
medium_multi	40GB	30