.. _`bio/lofreq/call`:

LOFREQ CALL
===========


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

simply call variants


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule lofreq:
        input:
            bam="data/{sample}.bam",
            bai="data/{sample}.bai"
        output:
            "calls/{sample}.vcf"
        log:
            "logs/lofreq_call/{sample}.log"
        params:
            ref="data/genome.fasta",
            extra=""
        threads: 8
        wrapper:
            "v3.0.4/bio/lofreq/call"

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

* ``samtools=1.18``
* ``lofreq=2.1.5``




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2018, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")
    ref = snakemake.params.get("ref", None)

    if ref is None:
        raise ValueError("A reference must be provided")

    bam_input = snakemake.input.bam
    bai_input = snakemake.input.bai

    if bam_input is None:
        raise ValueError("Missing bam input file!")

    if bai_input is None:
        raise ValueError("Missing bai input file!")

    output_file = snakemake.output[0]

    if output_file is None:
        raise ValueError("Missing output file")
    elif not len(snakemake.output) == 1:
        raise ValueError("Only expecting one output file: " + str(output_file) + "!")

    shell(
        "lofreq call-parallel "
        " --pp-threads {snakemake.threads}"
        " -f {ref}"
        " {bam_input}"
        " -o {output_file}"
        " {extra}"
        " {log}"
    )


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