.. _`bio/qualimap/bamqc`:

QUALIMAP RNASEQ
===============


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

Run qualimap bamqc to create a QC report for aligned NGS data data. It can be
used for WGS, WES, RNA, ChIP-Seq, etc.


**URL**: http://qualimap.conesalab.org/doc_html/analysis.html#bam-qc

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule qualimap:
        input:
            # BAM aligned, splicing-aware, to reference genome
            bam="mapped/a.bam",
        output:
            directory("qc/a"),
        log:
            "logs/qualimap/bamqc/a.log",
        # 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=4096,
        wrapper:
            "v3.0.1/bio/qualimap/bamqc"

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.


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

* ``qualimap=2.3``
* ``snakemake-wrapper-utils=0.6.2``

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

* BAM file of data aligned to genome

**Output:**

* QC report in TXT format (genome_results.txt)




Authors
-------

* Fritjof Lammers
* Brett Copeland


Code
----

.. code-block:: python

    __author__ = "Fritjof Lammers"
    __copyright__ = "Copyright 2022, Fritjof Lammers"
    __email__ = "f.lammers@dkfz.de"

    __license__ = "MIT"


    import os

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

    java_opts = get_java_opts(snakemake)

    if java_opts:
        java_opts_str = f'JAVA_OPTS="{java_opts}"'
    else:
        java_opts_str = ""

    # unset DISPLAY environment variable to avoid X11 error message issued by qualimap
    if os.environ.get("DISPLAY"):
        del os.environ["DISPLAY"]

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    shell(
        "{java_opts_str} qualimap bamqc {extra} "
        "-bam {snakemake.input.bam} "
        "-outdir {snakemake.output} "
        "{log}"
    )


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