.. _`bio/trinity`:

TRINITY
=======


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

Generate transcriptome assembly with Trinity


**URL**: https://github.com/trinityrnaseq/trinityrnaseq/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule trinity:
        input:
            left=["reads/reads.left.fq.gz", "reads/reads2.left.fq.gz"],
            right=["reads/reads.right.fq.gz", "reads/reads2.right.fq.gz"],
        output:
            dir=temp(directory("trinity_out_dir/")),
            fas="trinity_out_dir.Trinity.fasta",
            map="trinity_out_dir.Trinity.fasta.gene_trans_map",
        log:
            'logs/trinity/trinity.log',
        params:
            extra="",
        threads: 4
        resources:
            mem_gb=10,
        wrapper:
            "v3.0.4/bio/trinity"

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

* ``trinity=2.15.1``

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

* fastq files

**Output:**

* ``fas``: fasta containing assembly
* ``map``: gene transcripts map
* ``dir``: folder for intermediate results




Authors
-------

* Tessa Pierce


Code
----

.. code-block:: python

    """Snakemake wrapper for Trinity."""

    __author__ = "Tessa Pierce"
    __copyright__ = "Copyright 2018, Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    # Previous wrapper reserved 10 Gigabytes by default. This behaviour is
    # preserved below:
    max_memory = "10G"

    # Getting memory in megabytes, if java opts is not filled with -Xmx parameter
    # By doing so, backward compatibility is preserved
    if "mem_mb" in snakemake.resources.keys():
        # max_memory from trinity expects a value in gigabytes.
        rounded_mb_to_gb = int(snakemake.resources["mem_mb"] / 1024)
        max_memory = "{}G".format(rounded_mb_to_gb)

    # Getting memory in gigabytes, for user convenience. Please prefer the use
    # of mem_mb over mem_gb as advised in documentation.
    elif "mem_gb" in snakemake.resources.keys():
        max_memory = "{}G".format(snakemake.resources["mem_gb"])


    # allow multiple input files for single assembly
    left = snakemake.input.get("left")
    assert left is not None, "input-> left is a required input parameter"
    left = (
        [snakemake.input.left]
        if isinstance(snakemake.input.left, str)
        else snakemake.input.left
    )
    right = snakemake.input.get("right")
    if right:
        right = (
            [snakemake.input.right]
            if isinstance(snakemake.input.right, str)
            else snakemake.input.right
        )
        assert len(left) >= len(
            right
        ), "left input needs to contain at least the same number of files as the right input (can contain additional, single-end files)"
        input_str_left = " --left " + ",".join(left)
        input_str_right = " --right " + ",".join(right)
    else:
        input_str_left = " --single " + ",".join(left)
        input_str_right = ""

    input_cmd = " ".join([input_str_left, input_str_right])

    # infer seqtype from input files:
    seqtype = snakemake.params.get("seqtype")
    if not seqtype:
        if "fq" in left[0] or "fastq" in left[0]:
            seqtype = "fq"
        elif "fa" in left[0] or "fas" in left[0] or "fasta" in left[0]:
            seqtype = "fa"
        else:  # assertion is redundant - warning or error instead?
            assert (
                seqtype is not None
            ), "cannot infer 'fq' or 'fa' seqtype from input files. Please specify 'fq' or 'fa' in 'seqtype' parameter"


    shell(
        "Trinity {input_cmd} --CPU {snakemake.threads} "
        " --max_memory {max_memory} --seqType {seqtype} "
        " --output {snakemake.output.dir} {snakemake.params.extra} "
        " {log}"
    )


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