toil_strelka

Toil implementation of Strelka2 SNV Caller

Usage

This package uses docker to manage its dependencies, there are 2 ways of using it:

1. Running the container in single machine mode without --batchSystem support:

    # using docker
    docker run -it papaemmelab/toil_strelka --help
   
    # using singularity
    singularity run docker://papaemmelab/toil_strelka --help
   

2. Installing the python package from pypi and passing the container as a flag:

    # install package
    pip install toil_strelka
   
    # run with docker
    toil_strelka [TOIL-OPTIONS] [PIPELINE-OPTIONS]
        --docker papaemmelab/toil_strelka
        --volumes <local path> <container path>
        --batchSystem LSF
   
    # run with singularity
    toil_strelka [TOIL-OPTIONS] [PIPELINE-OPTIONS]
        --singularity docker://papaemmelab/toil_strelka
        --volumes <local path> <container path>
        --batchSystem LSF
   

See docker2singularity if you want to use a singularity image instead of using the docker:// prefix. If you want to run toil_strelka without a Docker/Singularity image, make sure {.../manta_installation_folder/bin} and {.../strelka_installation_folder/bin} are in the PATH.

Example

    toil_strelka \
        --singularity {singularity image} \
        --volumes /ifs /ifs \
        --workDir {recommend using $TMP_DIR} \
        jobstore \
        --stats \
        --disableCaching \
        --realTimeLogging \
        --batchSystem CustomLSF \
        --writeLogs {outdir}/logs_toil \
        --logFile {outdir}/head_job.toil \
        --logLevel "INFO" \
        --sequencing_method TGD \
        --normal {normal bam} \
        --tumor {tumor bam} \
        --outdir {outdir} \
        --reference {reference fasta file} \
        --bed {bed file}

Additional Options

Pipeline

As provided in Strelka docs:

Contributing

Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!

Credits

This package was created using Cookiecutter and the papaemmelab/cookiecutter-toil project template.