.. _`bio/dragmap/align`:

DRAGMAP
=======


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

Map reads with Dragmap.


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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule dragmap_align:
        input:
            reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
            idx="genome",
        output:
            "mapped/{sample}.bam",
        log:
            "logs/dragmap/{sample}.align.log",
        params:
            extra="",
            sorting="none",  # Can be 'none', 'samtools' or 'picard'.
            sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
            sort_extra="",  # Extra args for samtools/picard.
        threads: 8
        wrapper:
            "v3.0.4/bio/dragmap/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
---------------------

* ``dragmap=1.2``
* ``samtools=1.14``
* ``picard=2.26``
* ``snakemake-wrapper-utils=0.5.2``

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

* ``reads``: FASTQ file(s)
* ``idx``: reference hash table

**Output:**

* SAM/BAM/CRAM file



Params
------

* ``extra``: Optional parameters, besides `--num-threads`, and `-r`

* ``sorting``: Either `none`, `samtools` or `picard`

* ``sort_order``: Either `queryname` or `coordinate`

* ``sort_extra``: Optional parameters for samtools/picard




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

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


    from os import path
    import re
    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.samtools import get_samtools_opts
    from snakemake_wrapper_utils.java import get_java_opts


    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    samtools_opts = samtools_opts = get_samtools_opts(snakemake)
    java_opts = get_java_opts(snakemake)


    sort = snakemake.params.get("sorting", "none")
    sort_order = snakemake.params.get("sort_order", "coordinate")
    sort_extra = snakemake.params.get("sort_extra", "")


    n = len(snakemake.input.reads)
    assert (
        n == 1 or n == 2
    ), "input->reads must have 1 (single-end) or 2 (paired-end) elements."

    if n == 1:
        reads = "-1 {}".format(*snakemake.input.reads)
    else:
        reads = "-1 {} -2 {}".format(*snakemake.input.reads)


    index = snakemake.input.idx
    if isinstance(index, str):
        index = path.splitext(snakemake.input.idx)[0]
    else:
        index = path.splitext(snakemake.input.idx[0])[0]


    if sort_order not in {"coordinate", "queryname"}:
        raise ValueError("Unexpected value for sort_order ({})".format(sort_order))

    # Determine which pipe command to use for converting to bam or sorting.
    if sort == "none":
        # Simply convert to bam using samtools view.
        pipe_cmd = "samtools view {samtools_opts} {sort_extra} -"

    elif sort == "samtools":
        # Add name flag if needed.
        if sort_order == "queryname":
            sort_extra += " -n"

        # Sort alignments using samtools sort.
        pipe_cmd = "samtools sort {samtools_opts} {sort_extra} -"

    elif sort == "picard":
        # Sort alignments using picard SortSam.
        pipe_cmd = (
            "picard SortSam {java_opts} {sort_extra} --INPUT /dev/stdin"
            " --OUTPUT {snakemake.output[0]} --SORT_ORDER {sort_order} --TMP_DIR {tmpdir}"
        )
    else:
        raise ValueError("Unexpected value for params.sort ({})".format(sort))


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "(dragen-os"
            " --num-threads {snakemake.threads}"
            " -r {snakemake.input.idx}"
            " {reads}"
            " {extra}"
            " | " + pipe_cmd + ") {log}"
        )


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