.. _`bio/bismark/bismark2report`:

BISMARK2REPORT
==============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bismark/bismark2report?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/bismark/bismark2report

Generate graphical HTML report from Bismark reports (see https://github.com/FelixKrueger/Bismark/blob/master/bismark2report).



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    # Example: Pair-ended reads
    rule bismark2report_pe:
        input:
            alignment_report="bams/{sample}_{genome}_PE_report.txt",
            nucleotide_report="bams/{sample}_{genome}_pe.nucleotide_stats.txt",
            dedup_report="bams/{sample}_{genome}_pe.deduplication_report.txt",
            mbias_report="meth/{sample}_{genome}_pe.deduplicated.M-bias.txt",
            splitting_report="meth/{sample}_{genome}_pe.deduplicated_splitting_report.txt"
        output:
            html="qc/meth/{sample}_{genome}.bismark2report.html",
        log:
            "logs/qc/meth/{sample}_{genome}.bismark2report.html.log",
        params:
            skip_optional_reports=True
        wrapper:
            "v3.0.4/bio/bismark/bismark2report"

    # Example: Single-ended reads
    rule bismark2report_se:
        input:
            alignment_report="bams/{sample}_{genome}_SE_report.txt",
            nucleotide_report="bams/{sample}_{genome}.nucleotide_stats.txt",
            dedup_report="bams/{sample}_{genome}.deduplication_report.txt",
            mbias_report="meth/{sample}_{genome}.deduplicated.M-bias.txt",
            splitting_report="meth/{sample}_{genome}.deduplicated_splitting_report.txt"
        output:
            html="qc/meth/{sample}_{genome}.bismark2report.html",
        log:
            "logs/qc/meth/{sample}_{genome}.bismark2report.html.log",
        params:
            skip_optional_reports=True
        wrapper:
            "v3.0.4/bio/bismark/bismark2report"

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

* ``bowtie2=2.5.2``
* ``bismark=0.24.2``
* ``samtools=1.18``

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

* ``alignment_report``: Alignment report (if not specified bismark will try to find it current directory)
* ``nucleotide_report``: Optional Bismark nucleotide coverage report (if not specified bismark will try to find it current directory)
* ``dedup_report``: Optional deduplication report (if not specified bismark will try to find it current directory)
* ``splitting_report``: Optional Bismark methylation extractor report (if not specified bismark will try to find it current directory)
* ``mbias_report``: Optional Bismark methylation extractor report (if not specified bismark will try to find it current directory)

**Output:**

* ``html``: Output HTML file path, if batch mode isn't used.
* ``html_dir``: Output dir path for HTML reports if batch mode is used



Params
------

* ``skip_optional_reports``: Use 'true' of 'false' to not look for optional reports not mentioned in input section (passes 'none' to bismark2report)

* ``extra``: Any additional args




Authors
-------

* Roman Cherniatchik


Code
----

.. code-block:: python

    """Snakemake wrapper to generate graphical HTML report from Bismark reports."""
    # https://github.com/FelixKrueger/Bismark/blob/master/bismark2report

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

    import os
    from snakemake.shell import shell


    def answer2bool(v):
        return str(v).lower() in ("yes", "true", "t", "1")


    extra = snakemake.params.get("extra", "")
    cmds = ["bismark2report {extra}"]

    # output
    html_file = snakemake.output.get("html", "")
    output_dir = snakemake.output.get("html_dir", None)
    if output_dir is None:
        if html_file:
            output_dir = os.path.dirname(html_file)
    else:
        if html_file:
            raise ValueError(
                "bismark/bismark2report: Choose one: 'html=...' for a single dir or 'html_dir=...' for batch processing."
            )

    if output_dir is None:
        raise ValueError(
            "bismark/bismark2report: Output file or directory not specified. "
            "Use 'html=...' for a single dir or 'html_dir=...' for batch "
            "processing."
        )

    if output_dir:
        cmds.append("--dir {output_dir:q}")

    if html_file:
        html_file_name = os.path.basename(html_file)
        cmds.append("--output {html_file_name:q}")

    # reports
    reports = [
        "alignment_report",
        "dedup_report",
        "splitting_report",
        "mbias_report",
        "nucleotide_report",
    ]
    skip_optional_reports = answer2bool(
        snakemake.params.get("skip_optional_reports", False)
    )
    for report_name in reports:
        path = snakemake.input.get(report_name, "")
        if path:
            locals()[report_name] = path
            cmds.append("--{0} {{{1}:q}}".format(report_name, report_name))
        elif skip_optional_reports:
            cmds.append("--{0} 'none'".format(report_name))

    # log
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    cmds.append("{log}")

    # run shell command:
    shell(" ".join(cmds))


.. |nl| raw:: html

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