.. _`bio/igv-reports`:

IGV-REPORTS
===========


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

Create self-contained igv.js HTML pages.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule igv_report:
        input:
            fasta="minigenome.fa",
            vcf="variants.vcf",
            # any number of additional optional tracks, see igv-reports manual
            tracks=["alignments.bam"]
        output:
            "igv-report.html"
        params:
            extra=""  # optional params, see igv-reports manual
        log:
            "logs/igv-report.log"
        wrapper:
            "v3.0.1/bio/igv-reports"

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

* ``igv-reports=1.9.1``

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

* BAM, VCF, ...

**Output:**

* HTML




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    """Snakemake wrapper for igv-reports."""

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2019, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    tracks = snakemake.input.get("tracks", [])
    if tracks:
        if isinstance(tracks, str):
            tracks = [tracks]
        tracks = "--tracks {}".format(" ".join(tracks))

    shell(
        "create_report {extra} --standalone --output {snakemake.output[0]} {snakemake.input.vcf} {snakemake.input.fasta} {tracks} {log}"
    )


.. |nl| raw:: html

   <br>