.. _`bio/trim_galore/pe`:

TRIM_GALORE-PE
==============


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

Trim paired-end reads using trim_galore.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule trim_galore_pe:
        input:
            ["reads/{sample}.1.fastq.gz", "reads/{sample}.2.fastq.gz"],
        output:
            fasta_fwd="trimmed/{sample}_R1.fq.gz",
            report_fwd="trimmed/reports/{sample}_R1_trimming_report.txt",
            fasta_rev="trimmed/{sample}_R2.fq.gz",
            report_rev="trimmed/reports/{sample}_R2_trimming_report.txt",
        threads: 1
        params:
            extra="--illumina -q 20",
        log:
            "logs/trim_galore/{sample}.log",
        wrapper:
            "v3.0.1/bio/trim_galore/pe"


    rule trim_galore_pe_uncompressed:
        input:
            ["reads/{sample}_R1.fastq", "reads/{sample}_R2.fastq"],
        output:
            fasta_fwd="trimmed/{sample}_R1.fastq",
            report_fwd="trimmed/reports/{sample}_R1_trimming_report.txt",
            fasta_rev="trimmed/{sample}_R2.fastq",
            report_rev="trimmed/reports/{sample}_R2_trimming_report.txt",
        threads: 1
        params:
            extra="--illumina -q 20",
        log:
            "logs/trim_galore/{sample}.log",
        wrapper:
            "v3.0.1/bio/trim_galore/pe"

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
-----

* It is expected that the fastqc Snakemake wrapper be used in place
  of the `--fastqc` option.
* All output files must be placed in the same directory.


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

* ``trim-galore=0.6.10``

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

* two (paired-end) fastq files (can be gzip compressed)

**Output:**

* two trimmed (paired-end) fastq files
* two trimming reports



Params
------

* ``extra``: additional parameters




Authors
-------

* Kerrin Mendler


Code
----

.. code-block:: python

    """Snakemake wrapper for trimming paired-end reads using trim_galore."""

    __author__ = "Kerrin Mendler"
    __copyright__ = "Copyright 2018, Kerrin Mendler"
    __email__ = "mendlerke@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell
    import tempfile
    import re
    import os


    def report_filename(infile: str) -> str:
        """Infer report output file name from input
        >>> report_filename('reads/sample.1.fastq.gz')
        'sample.1.fastq.gz_trimming_report.txt
        >>> report_filename('reads/sample_R2.fastq.gz')
        'sample_R2.fastq.gz_trimming_report.txt
        """
        return os.path.basename(infile) + "_trimming_report.txt"


    def fasta_filename(infile: str, infix: str, out_gzip: bool) -> str:
        """Infer fasta output file name from input
        >>> fasta_filename('reads/sample.1.fq.gz', infix = '_val_1', out_gzip = False)
        'sample.1_val_1.fq.gz'
        >>> fasta_filename('reads/sample_R2.fastq', infix = '_val_2', out_gzip = True)
        'sample_R2_val_2.fq.gz'
        """
        base_input = os.path.basename(infile)
        suffix = ".gz" if out_gzip or infile.endswith(".gz") else ""
        REGEX_RULES = [r"\.fastq$", "\.fastq\.gz$", r"\.fq$", r"\.fq\.gz$"]
        for regex in REGEX_RULES:
            if re.search(regex, base_input):
                return re.sub(regex, f"{infix}.fq", base_input) + suffix
        return base_input + infix + suffix


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

    # Check that two input files were supplied
    n = len(snakemake.input)
    assert n == 2, "Input must contain 2 files. Given: %r." % n
    infile_fwd, infile_rev = snakemake.input[0:2]

    # Don't run with `--fastqc` flag
    if "--fastqc" in snakemake.params.get("extra", ""):
        raise ValueError(
            "The trim_galore Snakemake wrapper cannot "
            "be run with the `--fastqc` flag. Please "
            "remove the flag from extra params. "
            "You can use the fastqc Snakemake wrapper on "
            "the input and output files instead."
        )

    # Check that four output files were supplied
    m = len(snakemake.output)
    assert m == 4, "Output must contain 4 files. Given: %r." % m

    fasta_fwd, fasta_rev, report_fwd, report_rev = (
        snakemake.output.get(key)
        for key in ["fasta_fwd", "fasta_rev", "report_fwd", "report_rev"]
    )

    out_gzip = any((fasta_fwd.endswith("gz"), fasta_rev.endswith("gz")))
    if out_gzip:
        extra += " --gzip"

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "(trim_galore"
            " {extra}"
            " --cores {snakemake.threads}"
            " --paired"
            " -o {tmpdir}"
            " {infile_fwd} {infile_rev})"
            " {log}"
        )

        if report_fwd:
            shell(f"mv {tmpdir}/{report_filename(infile_fwd)} {report_fwd}")
        if report_rev:
            shell(f"mv {tmpdir}/{report_filename(infile_rev)} {report_rev}")

        if fasta_fwd:
            shell(
                f"mv {tmpdir}/{fasta_filename(infile_fwd, '_val_1', out_gzip)} {fasta_fwd}"
            )
        if fasta_rev:
            shell(
                f"mv {tmpdir}/{fasta_filename(infile_rev, '_val_2', out_gzip)} {fasta_rev}"
            )


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