.. _`bio/snpeff/annotate`:

SNPEFF
======


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

Annotate predicted effect of nucleotide changes with SnpEff.

**URL**: https://pcingola.github.io/SnpEff/se_introduction/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule snpeff:
        input:
            calls="{sample}.vcf", # (vcf, bcf, or vcf.gz)
            db="resources/snpeff/ebola_zaire" # path to reference db downloaded with the snpeff download wrapper
        output:
            calls="snpeff/{sample}.vcf",   # annotated calls (vcf, bcf, or vcf.gz)
            stats="snpeff/{sample}.html",  # summary statistics (in HTML), optional
            csvstats="snpeff/{sample}.csv" # summary statistics in CSV, optional
        log:
            "logs/snpeff/{sample}.log"
        resources:
            java_opts="-XX:ParallelGCThreads=10",
            mem_mb=4096
        wrapper:
            "v3.0.1/bio/snpeff/annotate"

    rule snpeff_nostats:
        input:
            calls="{sample}.vcf",
            db="resources/snpeff/ebola_zaire"
        output:
            calls="snpeff_nostats/{sample}.vcf",    # the main output file
            # if either "genes" or "stats" outputs are provided, both are created
        log:
            "logs/snpeff_nostats/{sample}.log"
        params:
            java_opts="-XX:ParallelGCThreads=10",
            extra=""                 # optional parameters
        resources:
            mem_mb=1024
        wrapper:
            "v3.0.1/bio/snpeff/annotate"

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

* ``snpeff=5.2``
* ``bcftools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* ``calls``: input VCF/BCF file
* ``db``: SnpEff database

**Output:**

* ``calls``: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
* ``genes``: genes output file (optional)
* ``stats``: stats file (optional)
* ``csvstats``: stats CSV file (optional)



Params
------

* ``java_opts``: additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

* ``extra``: additional program arguments.




Authors
-------

* Bradford Powell


Code
----

.. code-block:: python

    __author__ = "Bradford Powell"
    __copyright__ = "Copyright 2018, Bradford Powell"
    __email__ = "bpow@unc.edu"
    __license__ = "BSD"


    from snakemake.shell import shell
    from os import path
    import shutil
    import tempfile
    from pathlib import Path
    from snakemake_wrapper_utils.java import get_java_opts


    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    outcalls = snakemake.output.calls
    if outcalls.endswith(".vcf.gz"):
        outprefix = "| bcftools view -Oz"
    elif outcalls.endswith(".bcf"):
        outprefix = "| bcftools view -Ob"
    else:
        outprefix = ""

    incalls = snakemake.input[0]
    if incalls.endswith(".bcf"):
        incalls = "< <(bcftools view {})".format(incalls)

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

    data_dir = Path(snakemake.input.db).parent.resolve()

    stats = snakemake.output.get("stats", "")
    csvstats = snakemake.output.get("csvstats", "")
    csvstats_opt = "" if not csvstats else "-csvStats {}".format(csvstats)
    stats_opt = "-noStats" if not stats else "-stats {}".format(stats)

    reference = path.basename(snakemake.input.db)

    shell(
        "snpEff {java_opts} -dataDir {data_dir} "
        "{stats_opt} {csvstats_opt} {extra} "
        "{reference} {incalls} "
        "{outprefix} > {outcalls} {log}"
    )


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