.. _`bio/dada2/dereplicate-fastq`:

DADA2_DEREPLICATE_FASTQ
=======================


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   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/dada2/dereplicate-fastq

`DADA2 <https://benjjneb.github.io/dada2/index.html>`_
Dereplication of FASTQ files using dada2 ``derepFastq`` function. Optional parameters are documented in the `manual <https://www.bioconductor.org/packages/release/bioc/manuals/dada2/man/dada2.pdf#derepFastq>`_ and though the function is not introduced explicitly in the tutorial it is used in under the hood in the `learnErrors` `section <https://benjjneb.github.io/dada2/tutorial.html#learn-the-error-rates>`_.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule dada2_dereplicate_fastq:
        input:
        # Quality filtered FASTQ file
            "filtered/{fastq}.fastq"
        output:
        # Dereplicated sequences stored as `derep-class` object in a RDS file
            "uniques/{fastq}.RDS"
        log:
            "logs/dada2/dereplicate-fastq/{fastq}.log"
        wrapper:
            "v3.0.4/bio/dada2/dereplicate-fastq"

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

* ``bioconductor-dada2=1.28.0``

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

* a FASTQ file

**Output:**

* RDS file containing a ``derep-class`` object



Params
------

* ``optional arguments for ``derepFastq()``, please provide them as python ``key=value`` pairs``: 




Authors
-------

* Charlie Pauvert


Code
----

.. code-block:: R

    # __author__ = "Charlie Pauvert"
    # __copyright__ = "Copyright 2020, Charlie Pauvert"
    # __email__ = "cpauvert@protonmail.com"
    # __license__ = "MIT"

    # Snakemake wrapper for dereplicating FASTQ files using dada2 derepFastq function.

    # Sink the stderr and stdout to the snakemake log file
    # https://stackoverflow.com/a/48173272
    log.file<-file(snakemake@log[[1]],open="wt")
    sink(log.file)
    sink(log.file,type="message")

    library(dada2)

    # Prepare arguments (no matter the order)
    args<-list( fls = unlist(snakemake@input))
    # Check if extra params are passed
    if(length(snakemake@params) > 0 ){
           # Keeping only the named elements of the list for do.call()
           extra<-snakemake@params[ names(snakemake@params) != "" ]
           # Add them to the list of arguments
           args<-c(args, extra)
    } else{
        message("No optional parameters. Using default parameters from dada2::derepFastq()")
    }
    # Dereplicate
    uniques<-do.call(derepFastq, args)

    # Store as RDS file
    saveRDS(uniques,snakemake@output[[1]])

    # Proper syntax to close the connection for the log file
    # but could be optional for Snakemake wrapper
    sink(type="message")
    sink()



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