.. _`bio/hisat2/align`:

HISAT2 ALIGN
============


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/hisat2/align?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/hisat2/align

Map reads with hisat2.


**URL**: http://daehwankimlab.github.io/hisat2

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule hisat2_align:
        input:
            reads=["reads/{sample}_R1.fastq", "reads/{sample}_R2.fastq"],
            idx="index/",
        output:
            "mapped/{sample}.bam",
        log:
            "logs/hisat2_align_{sample}.log",
        params:
            extra="",
        threads: 2
        wrapper:
            "v3.0.1/bio/hisat2/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.


Notes
-----

* The `-S` flag must not be used since output is already directly piped to
  `samtools` for compression.
* The `--threads/-p` flag must not be used since threads is set separately
  via the snakemake `threads` directive.
* The wrapper does not yet handle SRA input accessions.
* No reference index files checking is done since the actual number of files
  may differ depending on the reference sequence size. This is also why
  the index is supplied in the `params` directive instead of the `input`
  directive.


Software dependencies
---------------------

* ``hisat2=2.2.1``
* ``samtools=1.18``

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

* ``reads``: either 1 or 2 FASTQ files with reads

**Output:**

* bam file with mapped reads



Params
------

* ``idx``: prefix of index file path (required)

* ``extra``: additional parameters




Authors
-------

* Wibowo Arindrarto


Code
----

.. code-block:: python

    __author__ = "Wibowo Arindrarto"
    __copyright__ = "Copyright 2016, Wibowo Arindrarto"
    __email__ = "bow@bow.web.id"
    __license__ = "BSD"


    import os
    from pathlib import Path
    from snakemake.shell import shell

    # Placeholder for optional parameters
    extra = snakemake.params.get("extra", "")
    # Run log
    log = snakemake.log_fmt_shell()

    # Input file wrangling
    reads = snakemake.input.get("reads")
    if isinstance(reads, str):
        input_flags = "-U {0}".format(reads)
    elif len(reads) == 1:
        input_flags = "-U {0}".format(reads[0])
    elif len(reads) == 2:
        input_flags = "-1 {0} -2 {1}".format(*reads)
    else:
        raise RuntimeError(
            "Reads parameter must contain at least 1 and at most 2" " input files."
        )

    ht2_files = Path(snakemake.input.idx).glob("*.ht2")
    idx_prefix = os.path.commonprefix(list(ht2_files)).rstrip(".")

    # Executed shell command
    shell(
        "(hisat2 {extra} "
        "--threads {snakemake.threads} "
        " -x {idx_prefix} {input_flags} "
        " | samtools view -Sbh -o {snakemake.output[0]} -) "
        " {log}"
    )


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