.. _`bio/qualimap/rnaseq`:

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


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

Run qualimap rnaseq to create a QC report for RNA-seq data.



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",
            # GTF containing transcript, gene, and exon data
            gtf="annotation.gtf"
        output:
            directory("qc/a")
        log:
            "logs/qualimap/rna-seq/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
        wrapper:
            "v3.0.1/bio/qualimap/rnaseq"

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
-----

* For more information, see http://qualimap.conesalab.org/doc_html/analysis.html#rnaseqqc.


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

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

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

* BAM file of RNA-seq data aligned to genome
* GTF file containing genome annotations

**Output:**

* QC report in html/pdf format




Authors
-------

* Brett Copeland


Code
----

.. code-block:: python

    __author__ = "Brett Copeland"
    __copyright__ = "Copyright 2021, Brett Copeland"
    __email__ = "brcopeland@ucsd.edu"
    __license__ = "MIT"


    import os

    from snakemake.shell import shell

    java_opts = snakemake.params.get("java_opts", "")
    if java_opts:
        java_opts_str = f'JAVA_OPTS="{java_opts}"'
    else:
        java_opts_str = ""
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    shell(
        "{java_opts_str} qualimap rnaseq {extra} "
        "-bam {snakemake.input.bam} -gtf {snakemake.input.gtf} "
        "-outdir {snakemake.output} "
        "{log}"
    )


.. |nl| raw:: html

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