.. _`bio/dragmap/build`:

DRAGMAP
=======


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

Build hash table for Dragmap read mapper.


**URL**: https://github.com/Illumina/DRAGMAP

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule dragmap_build:
        input:
            ref="{genome}.fasta",
        output:
            idx=multiext(
                "{genome}/",
                "hash_table.cfg",
                "hash_table.cfg.bin",
                "hash_table.cmp",
                "hash_table_stats.txt",
                "reference.bin",
                "ref_index.bin",
                "repeat_mask.bin",
                "str_table.bin",
            ),
        log:
            "logs/dragmap/{genome}.build.log",
        params:
            extra="",
        threads: 2
        wrapper:
            "v3.0.4/bio/dragmap/build"

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

* ``dragmap=1.3.0``

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

* ``ref``: Path to reference genome sequence (Fasta formatted)

**Output:**

* ``idx``: Path to reference hash table



Params
------

* ``extra``: Optional parameters, besides `--ht-num-threads`, `--build-hash-table`, `--ht-reference`, and `--output-directory`




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __license__ = "MIT"


    from pathlib import Path
    from snakemake.shell import shell


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


    # Prefix that should be used for the database
    prefix = Path(snakemake.output[0]).parent


    shell(
        "dragen-os"
        " --ht-num-threads {snakemake.threads}"
        " --build-hash-table true"
        " --ht-reference {snakemake.input[0]}"
        " --output-directory {prefix}"
        " {extra}"
        " {log}"
    )


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