toil_conpair

📊 Compare targets against references using Conpair.

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 leukgen/toil_conpair --help
   
    # using singularity
    singularity run docker://leukgen/toil_conpair --help
   

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

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

See docker2singularity if you want to use a singularity image instead of using the docker:// prefix.

Example

toil_conpair \
    jobstore \
    --docker leukgen/toil_conpair \
    --volumes {local path} {container path} \
    --disableCaching \
    --batchSystem LSF \
    --writeLogs {outdir}/logs_toil \
    --logFile {outdir}/head_job.toil \
    --setEnv TOIL_LSF_JOBNAME='Conpair Pipeline' \
    --outdir {outdir} \
    --reference {reference id} {reference bam} \
    --reference {reference2 id} {reference2 bam} \
    --target {target id} {target bam} \
    --target {target2 id} {target2 bam} \
    --fasta {reference genome fasta} \
    --marker_bed {marker bed file} \
    --marker_txt {marker txt file} \
    --mismatched_pairs \
    --use_het

Contributing

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

Credits

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