.. _`bio/samtools/fastq/interleaved`:

SAMTOOLS FASTQ INTERLEAVED
==========================


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

Convert a bam file back to unaligned reads in a single fastq file with samtools. For paired end reads, this results in an unsorted interleaved file.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule samtools_fastq_interleaved:
        input:
            "mapped/{sample}.bam",
        output:
            "reads/{sample}.fq",
        log:
            "{sample}.interleaved.log",
        params:
            " ",
        threads: 3
        wrapper:
            "v3.0.1/bio/samtools/fastq/interleaved"

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 `extra` param allows for additional program arguments (not `-@/--threads` or `-o`).
* For more information see, http://www.htslib.org/doc/samtools-fasta.html


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

* ``samtools=1.14``
* ``snakemake-wrapper-utils=0.5.2``




Authors
-------

* David Laehnemann
* Victoria Sack
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "David Laehnemann, Victoria Sack"
    __copyright__ = "Copyright 2018, David Laehnemann, Victoria Sack"
    __email__ = "david.laehnemann@hhu.de"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell
    from snakemake_wrapper_utils.samtools import get_samtools_opts

    samtools_opts = get_samtools_opts(
        snakemake, parse_write_index=False, parse_output_format=False
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    shell("samtools fastq {samtools_opts} {extra} {snakemake.input[0]} {log}")


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