.. _`bio/prosolo/control-fdr`:

PROSOLO FDR CONTROL
===================


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

ProSolo can control the false discovery rate of any combination of its defined single cell events (like the presence of an alternative allele or the dropout of an allele).



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule prosolo_fdr_control:
        input:
             "variant_calling/{sc}.{bulk}.prosolo.bcf"
        output:
             "fdr_control/{sc}.{bulk}.prosolo.fdr.bcf"
        threads:
            1
        params:
            # comma-separated set of events for whose (joint)
            # false discovery rate you want to control
            events = "ADO_TO_REF,HET",
            # false discovery rate to control for
            fdr = 0.05
        log:
            "logs/prosolo_{sc}_{bulk}.fdr.log"
        wrapper:
            "v3.0.4/bio/prosolo/control-fdr"

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

* ``prosolo=0.6.1``

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

* Variants called with prosolo in vcf or bcf format, including the fine-grained posterior probabilities for single cell events.

**Output:**

* bcf file with all variants that satisfy the chosen false discovery rate threshold with regard to the specified events.




Authors
-------

* David Lähnemann


Code
----

.. code-block:: python

    """Snakemake wrapper for ProSolo FDR control"""

    __author__ = "David Lähnemann"
    __copyright__ = "Copyright 2020, David Lähnemann"
    __email__ = "david.laehnemann@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    shell(
        "( prosolo control-fdr"
        " {snakemake.input}"
        " --events {snakemake.params.events}"
        " --var SNV"
        " --fdr {snakemake.params.fdr}"
        " --output {snakemake.output} )"
        "{log} "
    )


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