.. _`bio/pbmm2/align`:

PBMM2 ALIGN
===========


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

Align reads 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_align:
        input:
            reference="target/{reference}.fasta", # can be either genome index or genome fasta
            query="{query}.bam", # can be either unaligned bam, fastq, or fasta
        output:
            bam="aligned/{query}.{reference}.bam",
            index="aligned/{query}.{reference}.bam.bai",
        log:
            "logs/pbmm2_align/{query}.{reference}.log",
        params:
            preset="CCS", # SUBREAD, CCS, HIFI, ISOSEQ, UNROLLED
            sample="", # sample name for @RG header
            extra="--sort", # optional additional args
            loglevel="INFO",
        threads: 12
        wrapper:
            "v3.0.1/bio/pbmm2/align"

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"

    import tempfile
    from snakemake.shell import shell


    extra = snakemake.params.get("extra", "")
    tmp_root = snakemake.params.get("tmp_root", None)
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    with tempfile.TemporaryDirectory(dir=tmp_root) as tmp_dir:
        shell(
            """
            (TMPDIR={tmp_dir}; \
            pbmm2 align --num-threads {snakemake.threads} \
                --preset {snakemake.params.preset} \
                --sample {snakemake.params.sample} \
                --log-level {snakemake.params.loglevel} \
                {extra} \
                {snakemake.input.reference} \
                {snakemake.input.query} \
                {snakemake.output.bam}) {log}
            """
        )


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