.. _`bio/dada2/quality-profile`:

DADA2_QUALITY_PROFILES
======================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/dada2/quality-profile?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/dada2/quality-profile

`DADA2 <https://benjjneb.github.io/dada2/index.html>`_
Plotting the quality profile of reads using dada2 ``plotQualityProfile`` function. The function is introduced in the dedicated tutorial `section <https://benjjneb.github.io/dada2/tutorial.html#inspect-read-quality-profiles>`_.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule dada2_quality_profile_se:
        input:
            # FASTQ file without primers sequences
            "trimmed/{sample}.{orientation}.fastq"
        output:
            "reports/dada2/quality-profile/{sample}.{orientation}-quality-profile.png"
        log:
            "logs/dada2/quality-profile/{sample}.{orientation}-quality-profile-se.log"
        wrapper:
            "v3.0.4/bio/dada2/quality-profile"

    rule dada2_quality_profile_pe:
        input:
            # FASTQ file without primers sequences
            expand("trimmed/{{sample}}.{orientation}.fastq",orientation=[1,2])
        output:
            "reports/dada2/quality-profile/{sample}-quality-profile.png"
        log:
            "logs/dada2/quality-profile/{sample}-quality-profile-pe.log"
        wrapper:
            "v3.0.4/bio/dada2/quality-profile"

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 (potentially compressed) without primers sequences

**Output:**

* A PNG file of the quality plot




Authors
-------

* Charlie Pauvert


Code
----

.. code-block:: R

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

    # Snakemake wrapper for plotting the quality profile of reads using dada2 plotQualityProfile 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)

    # Plot the quality profile for a given FASTQ file or a list of files
    pquality<-plotQualityProfile(unlist(snakemake@input))

    # Write the plots to files
    library(ggplot2)
    ggsave(snakemake@output[[1]], pquality, width = 4, height = 3, dpi = 300)

    # 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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