.. _`bio/salmon/index`:

SALMON_INDEX
============


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

Index a transcriptome assembly with salmon


**URL**: https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule salmon_index:
        input:
            sequences="assembly/transcriptome.fasta",
        output:
            multiext(
                "salmon/transcriptome_index/",
                "complete_ref_lens.bin",
                "ctable.bin",
                "ctg_offsets.bin",
                "duplicate_clusters.tsv",
                "info.json",
                "mphf.bin",
                "pos.bin",
                "pre_indexing.log",
                "rank.bin",
                "refAccumLengths.bin",
                "ref_indexing.log",
                "reflengths.bin",
                "refseq.bin",
                "seq.bin",
                "versionInfo.json",
            ),
        log:
            "logs/salmon/transcriptome_index.log",
        threads: 2
        params:
            # optional parameters
            extra="",
        wrapper:
            "v3.0.1/bio/salmon/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
---------------------

* ``salmon=1.10.2``

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

* ``sequences``: Path to sequences to index with Salmon. This can be transcriptome sequences or gentrome.
* ``decoys``: Optional path to decoy sequences name, in case the above `sequence` was a gentrome.

**Output:**

* indexed assembly



Params
------

* ``extra``: Optional parameters besides `--tmpdir`, `--threads`, and IO.




Authors
-------

* Tessa Pierce
* Thibault Dayris


Code
----

.. code-block:: python

    """Snakemake wrapper for Salmon Index."""

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

    from os.path import dirname
    from snakemake.shell import shell
    from tempfile import TemporaryDirectory

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

    decoys = snakemake.input.get("decoys", "")
    if decoys:
        decoys = f"--decoys {decoys}"

    output = snakemake.output
    if len(output) > 1:
        output = dirname(snakemake.output[0])

    with TemporaryDirectory() as tempdir:
        shell(
            "salmon index "
            "--transcripts {snakemake.input.sequences} "
            "--index {output} "
            "--threads {snakemake.threads} "
            "--tmpdir {tempdir} "
            "{decoys} "
            "{extra} "
            "{log}"
        )


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