.. _`bio/bismark/deduplicate_bismark`:

DEDUPLICATE_BISMARK
===================


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

Deduplicate Bismark Bam Files


**URL**: https://github.com/FelixKrueger/Bismark/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule deduplicate_bismark:
        input: "bams/{sample}.bam"
        output:
            bam="bams/{sample}.deduplicated.bam",
            report="bams/{sample}.deduplication_report.txt",
        log:
            "logs/bams/{sample}.deduplicated.log",
        params:
            extra=""  # optional params string
        wrapper:
            "v5.5.2/bio/bismark/deduplicate_bismark"

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

* ``bismark=0.24.2``
* ``bowtie2=2.5.4``
* ``samtools=1.21``

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

* path to one or multiple \*.bam files aligned by Bismark, if multiple passed '--multiple' argument will be added automatically.

**Output:**

* ``bam``: Result bam file path. The file will be renamed if differs from `NAME.deduplicated.bam` for given 'NAME.bam' input.
* ``report``: Result report path. The file will be renamed if differs from `NAME.deduplication_report.txt` for given 'NAME.bam' input.



Params
------

* ``extra``: Additional deduplicate_bismark args




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper for Bismark aligned reads deduplication using deduplicate_bismark."""

    # https://github.com/FelixKrueger/Bismark/blob/master/deduplicate_bismark

    __author__ = "Roman Chernyatchik"
    __copyright__ = "Copyright (c) 2019 JetBrains"
    __email__ = "roman.chernyatchik@jetbrains.com"
    __license__ = "MIT"

    import os
    from snakemake.shell import shell

    bam_path = snakemake.output.get("bam", None)
    report_path = snakemake.output.get("report", None)
    if not bam_path or not report_path:
        raise ValueError(
            "bismark/deduplicate_bismark: Please specify both 'bam=..' and 'report=..' paths in output section"
        )

    output_dir = os.path.dirname(bam_path)
    if output_dir != os.path.dirname(report_path):
        raise ValueError(
            "bismark/deduplicate_bismark: BAM and Report files expected to have the same parent directory"
            " but was {} and {}".format(bam_path, report_path)
        )

    arg_output_dir = "--output_dir '{}'".format(output_dir) if output_dir else ""
    arg_multiple = "--multiple" if len(snakemake.input) > 1 else ""

    params_extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    log_append = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
    shell(
        "deduplicate_bismark {params_extra} --bam {arg_multiple}"
        " {arg_output_dir} {snakemake.input} {log}"
    )

    # Move outputs into proper position.
    fst_input_filename = os.path.basename(snakemake.input[0])
    fst_input_basename = os.path.splitext(fst_input_filename)[0]
    prefix = os.path.join(output_dir, fst_input_basename)

    deduplicated_bam_actual_name = prefix + ".deduplicated.bam"
    if arg_multiple:
        # bismark does it exactly like this:
        deduplicated_bam_actual_name = deduplicated_bam_actual_name.replace(
            "deduplicated", "multiple.deduplicated", 1
        )

    expected_2_actual_paths = [
        (bam_path, deduplicated_bam_actual_name),
        (
            report_path,
            prefix + (".multiple" if arg_multiple else "") + ".deduplication_report.txt",
        ),
    ]
    for exp_path, actual_path in expected_2_actual_paths:
        if exp_path and (exp_path != actual_path):
            shell("mv {actual_path:q} {exp_path:q} {log_append}")


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