.. _`bio/rbt/csvreport`:

RBT CSV-REPORT
==============


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

Creates an html report of qc data stored in a csv file. For more details, visit https://github.com/rust-bio/rust-bio-tools


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule csv_report:
        input:
            # a csv formatted file containing the data for the report
            "report.csv",
        output:
            # path to the resulting report directory
            directory("qc_data"),
        params:
            extra="--sort-column 'contig length'",
        log:
            "logs/rbt-csv-report",
        wrapper:
            "v3.0.1/bio/rbt/csvreport"

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

* ``rust-bio-tools=0.42.0``

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

* A csv file containing the qc report

**Output:**

* QC report folder including html document and .xlsx file




Authors
-------

* Jan Forster


Code
----

.. code-block:: python

    __author__ = "Jan Forster"
    __copyright__ = "Copyright 2021, Jan Forster"
    __email__ = "jan.forster@uk-essen.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    shell("rbt csv-report {snakemake.input} {snakemake.output} {extra} {log}")


.. |nl| raw:: html

   <br>