.. _`bio/vsearch`:

VSEARCH
=======


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

Versatile open-source tool for microbiome analysis.


**URL**: https://github.com/torognes/vsearch

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule vsearch_cluster_fast:
        input:
            cluster_fast="reads/{sample}.fasta",
        output:
            profile="out/cluster_fast/{sample}.profile",
        log:
            "logs/vsearch/cluster_fast/{sample}.log",
        params:
            extra="--id 0.2 --sizeout --minseqlength 5",
        threads: 1
        wrapper:
            "v3.0.1/bio/vsearch"


    rule vsearch_maskfasta:
        input:
            maskfasta="reads/{sample}.fasta",
        output:
            output="out/maskfasta/{sample}.fasta",
        log:
            "logs/vsearch/maskfasta/{sample}.log",
        params:
            extra="--hardmask",
        threads: 1
        wrapper:
            "v3.0.1/bio/vsearch"


    rule vsearch_fastx_uniques:
        input:
            fastx_uniques="reads/{sample}.fastq",
        output:
            fastqout="out/fastx_uniques/{sample}.fastq",
        log:
            "logs/vsearch/fastx_uniques/{sample}.log",
        params:
            extra="--strand both --minseqlength 5",
        threads: 2
        wrapper:
            "v3.0.1/bio/vsearch"


    rule vsearch_fastx_uniques_gzip:
        input:
            fastx_uniques="reads/{sample}.fastq",
        output:
            fastqout="out/fastx_uniques/{sample}.fastq.gz",
        log:
            "logs/vsearch/fastx_uniques/{sample}.log",
        params:
            extra="--strand both --minseqlength 5",
        threads: 2
        wrapper:
            "v3.0.1/bio/vsearch"


    rule vsearch_fastx_uniques_bzip2:
        input:
            fastx_uniques="reads/{sample}.fastq",
        output:
            fastqout="out/fastx_uniques/{sample}.fastq.bz2",
        log:
            "logs/vsearch/fastx_uniques/{sample}.log",
        params:
            extra="--strand both --minseqlength 5",
        threads: 2
        wrapper:
            "v3.0.1/bio/vsearch"


    rule vsearch_fastq_convert:
        input:
            fastq_convert="reads/{sample}.fastq",
        output:
            fastqout="out/fastq_convert/{sample}.fastq",
        log:
            "logs/vsearch/fastq_convert/{sample}.log",
        params:
            extra="--fastq_ascii 33 --fastq_asciiout 64",
        threads: 2
        wrapper:
            "v3.0.1/bio/vsearch"

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
-----

* Keys for `input` and `output` files need to match `vsearch` arguments, (e.g. input) `uchime_denovo`, `cluster_fast`, `fastx_uniques`, `maskfasta`, `fastq_convert`, `fastq_mergepairs`, or (e.g. output) `chimeras`, `fastaout`, `fastqout`, `output`.


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

* ``vsearch=2.25.0``
* ``gzip``
* ``bzip2``

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

* input file(s)

**Output:**

* output file(s)



Params
------

* ``extra``: additional program arguments




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2021, Filipe G. Vieira"
    __license__ = "MIT"

    from snakemake.shell import shell


    extra = snakemake.params.get("extra", "")
    if snakemake.log:
        log = f"--log {snakemake.log}"


    input = " ".join([f"--{key} {value}" for key, value in snakemake.input.items()])


    out_list = list()
    for key, value in snakemake.output.items():
        if value.endswith(".gz"):
            out_list.append(f"--{key} /dev/stdout | gzip > {value}")
        elif value.endswith(".bz2"):
            out_list.append(f"--{key} /dev/stdout | bzip2 > {value}")
        else:
            out_list.append(f"--{key} {value}")

    # Check which output files are to be compressed
    out_gz = [out.endswith(".gz") for out in out_list]
    out_bz2 = [out.endswith(".bz2") for out in out_list]
    assert sum(out_gz + out_bz2) <= 1, "only one output can be compressed"

    # Move compressed file (if any) to last
    output = [out for _, out in sorted(zip(out_gz or out_bz2, out_list))]


    shell("vsearch --threads {snakemake.threads} {input} {extra} {log} {output}")


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