.. _`bio/strelka/somatic`:

STRELKA
=======


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

Strelka calls somatic and germline small variants from mapped sequencing reads



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule strelka:
        input:
            # The normal bam and its index
            # are optional input
            # normal = "data/b.bam",
            # normal_index = "data/b.bam.bai"
            tumor="data/{tumor}.bam",
            tumor_index="data/{tumor}.bam.bai",
            fasta="data/genome.fasta",
            fasta_index="data/genome.fasta.fai",
        output:
            # Strelka output - can be directory or full file path
            directory("{tumor}_vcf"),
        threads: 1
        params:
            run_extra="",
            config_extra="",
        log:
            "logs/strelka_{tumor}.log",
        wrapper:
            "v3.0.1/bio/strelka/somatic"

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
---------------------

* ``strelka=2.9.10``

Input/Output
------------
**Input:**

* A tumor bam file, with its index.
* A reference genome sequence in fasta format, with its index.
* An optional normal bam file for somatic calling, with its index.

**Output:**

* Statistics about calling results
* Variants called




Authors
-------

* Thibault Dayris
* Christopher Schröder


Code
----

.. code-block:: python

    """Snakemake wrapper for Strelka"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2019, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from pathlib import Path
    from snakemake.shell import shell
    from snakemake.utils import makedirs

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    config_extra = snakemake.params.get("config_extra", "")
    run_extra = snakemake.params.get("run_extra", "")

    # If a normal bam is given in input,
    # then it should be provided in the input
    # block, so Snakemake will perform additional
    # tests on file existance.
    normal = (
        "--normalBam {}".format(snakemake.input["normal"])
        if "normal" in snakemake.input.keys()
        else ""
    )

    if snakemake.output[0].endswith("vcf.gz"):
        run_dir = Path(snakemake.output[0]).parents[2]
    else:
        run_dir = snakemake.output

    shell(
        "(configureStrelkaSomaticWorkflow.py "  # Configuration script
        "{normal} "  # Path to normal bam (if any)
        "--tumorBam {snakemake.input.tumor} "  # Path to tumor bam
        "--referenceFasta {snakemake.input.fasta} "  # Path to fasta file
        "--runDir {run_dir} "  # Path to output directory
        "{config_extra} "  # Extra parametersfor configuration
        " && "
        "{run_dir}/runWorkflow.py "  # Run the pipeline
        "--mode local "  # Stop internal job submission
        "--jobs {snakemake.threads} "  # Nomber of threads
        "{run_extra}) "  # Extra parameters for runWorkflow
        "{log}"  # Logging behaviour
    )


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