Mendelian Randomization Analysis Pipeline: mr-seek

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mr-seek 🔬

Mendelian randomization pipeline

This is the home of the pipeline, mr-seek. Its long-term goals: to perform Mendelian randomization analysis like no pipeline before!

Overview

Welcome to mr-seek! Before getting started, we highly recommend reading through mr-seek's documentation .

The ./mr-seek pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

mr-seek run : Run the mr-seek pipeline with your input files.
mr-seek unlock : Unlocks a previous runs output directory.
mr-seek cache : Cache remote resources locally, coming soon!

mr-seek is a comprehensive an awesome mendelian randomization pipeline. It relies on technologies like Singularity1 to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake2 , a flexible and scalable workflow management system, to submit jobs to a cluster.

The pipeline is compatible with data generated from Illumina short-read sequencing technologies. As input, it accepts a set of QTL files and outcome phenotypes and can be run on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.

Before getting started, we highly recommend reading through the usage section of each available sub command.

For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github .

Dependencies

Requires: singularity>=3.5 snakemake>=6.0

At the current moment, the pipeline uses a mixture of enviroment modules and docker images; however, this will be changing soon! In the very near future, the pipeline will only use docker images. With that being said, snakemake and singularity must be installed on the target system. Snakemake orchestrates the execution of each step in the pipeline. To guarantee the highest level of reproducibility, each step of the pipeline will rely on versioned images from DockerHub . Snakemake uses singularity to pull these images onto the local filesystem prior to job execution, and as so, snakemake and singularity will be the only two dependencies in the future.

Installation

Please clone this repository to your local filesystem using the following command:

# Clone Repository from Github
git clone https://github.com/OpenOmics/mr-seek.git
# Change your working directory
cd mr-seek/
# Add dependencies to $PATH
# Biowulf users should run
module load snakemake singularity
# Get usage information
./mr-seek -h

Contribute

This site is a living document, created for and by members like you. mr-seek is maintained by the members of OpenOmics and is improved by continuous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository .

References

1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.

Code Snippets

shell:
  """
  cd {params.tmpdir}
  python3 {params.snp_script} -o "{params.sample}.convert.tsv" -i "{params.neale_path}/{params.sample}.tsv.bgz" -t {params.threshold} -p {params.population} --filter &&
  mv "filter.{params.sample}.convert.tsv.gz" "{output.gwas}" || touch "{output.gwas}" "{workpath}/{params.sample}.error"
  """

SnakeMake From line 76 of rules/mr.smk

shell:
    """
    Rscript {params.script} --query {input.query} \\
        --manifest {params.manifest} \\
        --output {output.phenotype_list} \\
        --metadata {output.phenotype_metadata}
    """

SnakeMake From line 94 of rules/mr.smk

shell:
    """
    Rscript {params.script} --query {input.query} \\
        --pop {params.pop_flag} \\
        --manifest {params.manifest} \\
        --output {output.phenotype_list} \\
        --error {params.error_log} \\
        --metadata {output.phenotype_metadata}
    """

SnakeMake From line 115 of rules/mr.smk

shell:
    """
    Rscript {params.script} \\
        --workdir {params.outdir} \\
        --exp "{params.exposure}" \\
        --out "{params.outcome}" \\
        --pop {params.pop_flag} \\
        --path {params.path} \\
        --error {params.error_log} \\
        {params.add_flag} \\
     > {log} 2>&1
    """

SnakeMake From line 150 of rules/mr.smk

shell:
    """
    Rscript {params.script} --res {input.res} \\
        --data {input.data} \\
        --single {input.single} \\
        --loo {input.loo} \\
        --heterogeneity {input.heterogeneity} \\
        --pleiotropy {input.pleiotropy} \\
        --metadata {input.phenotype_metadata} \\
        --out {output.rds} \\
        --version {input.sessionInfo} \\
        --failed {params.error} \\
        --include_data \\
        {params.additional_flags} \\
        > {log} 2>&1
    """