.. _`bio/picard/samtofastq`:

PICARD SAMTOFASTQ
=================


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

Converts a SAM or BAM file to FASTQ.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bam_to_fastq:
        input:
            "mapped/{sample}.bam",
        output:
            fastq1="reads/{sample}.R1.fastq",
            fastq2="reads/{sample}.R2.fastq",
        log:
            "logs/picard/sam_to_fastq/{sample}.log",
        params:
            extra="",  # optional: Extra arguments for picard.
        # optional specification of memory usage of the JVM that snakemake will respect with global
        # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
        # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
        # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/picard/samtofastq"

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.


Notes
-----

* The `java_opts` param allows for 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).
* The `extra` param allows for additional program arguments.
* `--TMP_DIR` is automatically set by `resources.tmpdir`
* For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq


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

* ``picard=3.1.1``
* ``snakemake-wrapper-utils=0.6.2``

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

* sam/bam file

**Output:**

* fastq files.




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    """Snakemake wrapper for picard SortSam."""

    __author__ = "Julian de Ruiter"
    __copyright__ = "Copyright 2017, Julian de Ruiter"
    __email__ = "julianderuiter@gmail.com"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts


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

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

    fastq1 = snakemake.output.fastq1
    fastq2 = snakemake.output.get("fastq2", None)
    fastq_unpaired = snakemake.output.get("unpaired_fastq", None)

    if not isinstance(fastq1, str):
        raise ValueError("f1 needs to be provided")

    output = f"--FASTQ {fastq1}"

    if isinstance(fastq2, str):
        output += f" --SECOND_END_FASTQ {fastq2}"

    if isinstance(fastq_unpaired, str):
        if not isinstance(fastq2, str):
            raise ValueError("f2 is required if fastq_unpaired is set")

        output += f" --UNPAIRED_FASTQ {fastq_unpaired}"

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "picard SamToFastq"
            " {java_opts} {extra}"
            " --INPUT {snakemake.input[0]}"
            " --TMP_DIR {tmpdir}"
            " {output}"
            " {log}"
        )


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