.. _`bio/open-cravat/run`:

OPENCRAVAT RUN
==============

.. image:: https://img.shields.io/badge/blacklisted-Fails%20to%20get%20wghg19-1.0.3%20with%20HTTP%20error-red

.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/open-cravat/run?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/open-cravat/run

Runs OpenCRAVAT. Annotate variant calls with OpenCRAVAT. For more details, see https://github.com/KarchinLab/open-cravat/wiki.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule opencravat:
        input:
            'example_input.tsv',
            'modules/commons/hg38wgs',
            'modules/converters/cravat-converter',
            'modules/mappers/hg38',
            'modules/annotators/biogrid',
            'modules/annotators/clinvar',
            'modules/postaggregators/tagsampler',
            'modules/postaggregators/varmeta',
            'modules/postaggregators/vcfinfo',
            'modules/reporters/excelreporter',
            'modules/reporters/tsvreporter',
            'modules/reporters/csvreporter',
        output:
            'example_input.tsv.xlsx',
            'example_input.tsv.variant.tsv',
            'example_input.tsv.variant.csv'
        log:
            "logs/open-cravat/run.log"
        threads: 1 # set number of threads for parallel processing
        wrapper:
            "v3.0.1/bio/open-cravat/run"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``open-cravat=2.4.1``




Authors
-------

* Rick Kim


Code
----

.. code-block:: python

    __author__ = "Rick Kim"
    __copyright__ = "Copyright 2020, Rick Kim"
    __license__ = "GPLv3"

    from snakemake.shell import shell
    import os

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    inputfiles = []
    annotators = []
    reporters = []
    modules_dir = set()
    for v in snakemake.input:
        if os.path.isfile(v):
            inputfiles.append(v)
        elif os.path.isdir(v):
            (module_group_dir, module_name) = os.path.split(v)
            (in_modules_dir, module_group) = os.path.split(module_group_dir)
            modules_dir.add(in_modules_dir)
            if module_group == "annotators":
                annotators.append(module_name)
            elif module_group == "reporters" and module_name.endswith("reporter"):
                reporters.append(module_name[:-8])
    if len(modules_dir) > 1:
        print(f'Multiple modules directory detected: {",".join(list(modules_dir))}')
        exit()
    cmd = ["oc", "run"]
    cmd.extend(inputfiles)
    genome = snakemake.params.get("genome", "hg38")
    mp = snakemake.threads
    cmd.extend(["-l", genome])
    cmd.extend(["--mp", str(mp)])
    if len(annotators) > 0:
        cmd.append("-a")
        cmd.extend(annotators)
    if len(reporters) > 0:
        cmd.append("-t")
        cmd.extend(reporters)
    extra = snakemake.params.get("extra", "")
    if len(extra) > 0 and type(extra) == str:
        cmd.extend(extra.split(" "))
    shell("{cmd} {log}")


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