docker_execution.md

Conda based execution

You can run the MAGMA pipeline using the Conda based package manager to install all the prerequisite softwares.

The conda environments are expected by the conda_local profile of the pipeline, to be created within MAGMA/conda_envs directory

NOTE If you do have access to Singularity or Podman, then owing to their compatibility with Docker, you can still use the MAGMA Docker containers mentioned docker.config.

Here's the command which should be used

nextflow run 'https://github.com/TORCH-Consortium/MAGMA' \
		 -name experiment-1 \
		 -params-file experiment-1.yml \
		 -profile conda_local \
		 -c custom.config \
		 -r v1.0.0 

You could use -r option of Nextflow for working with any specific version/branch of the pipeline.

---

And here are the contents of the following files

• experiment-1.yml => You could name it as per your convenience. Here's a sample params yaml file

input_samplesheet: "/full/path/to/samplesheet.csv"
outdir :  "/full/path/to/magma-results"
optimize_variant_recalibration :  false
compute_minor_variants :  true
dataset_is_not_contaminated :  true
conda_envs_location :  "/home/magma-runs/magma/conda_envs"

• custom.config => Ideally this file should only contain hardware level configurations such as

process {
    errorStrategy = { task.attempt < 3 ? 'retry' : 'ignore' }

    time = '1h'
    cpus = 8
    memory = 8.GB

   withName:FASTQ_VALIDATOR {
      cpus = 2
      memory = 4.GB
   }
}