.. _`bio/pbmm2/index`:

PBMM2 INDEX
===========


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/pbmm2/index?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/pbmm2/index

Indexes a reference using pbmm2, a minimap2 SMRT wrapper for PacBio data https://github.com/PacificBiosciences/pbmm2/


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule pbmm2_index:
        input:
            reference="target/{reference}.fasta",
        output:
            "target/{reference}.mmi",
        log:
            "logs/pbmm2_index/{reference}.log",
        params:
            preset="CCS", # SUBREAD, CCS, HIFI, ISOSEQ, UNROLLED
            extra="", # optional additional args
        threads: 8
        wrapper:
            "v3.0.4/bio/pbmm2/index"

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

* ``pbmm2=1.13.1``




Authors
-------

* William Rowell


Code
----

.. code-block:: python

    __author__ = "William Rowell"
    __copyright__ = "Copyright 2020, William Rowell"
    __email__ = "wrowell@pacb.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    shell(
        """
        (pbmm2 index \
        --num-threads {snakemake.threads} \
        --preset {snakemake.params.preset} \
        --log-level DEBUG \
        {extra} \
        {snakemake.input.reference} {snakemake.output}) {log}
        """
    )


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