.. _`bio/sra-tools/fasterq-dump`:

SRA-TOOLS FASTERQ-DUMP
======================


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

Download FASTQ files from SRA.


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule get_fastq_pe:
        output:
            # the wildcard name must be accession, pointing to an SRA number
            "data/pe/{accession}_1.fastq",
            "data/pe/{accession}_2.fastq",
        log:
            "logs/pe/{accession}.log"
        params:
            extra="--skip-technical"
        threads: 6  # defaults to 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"


    rule get_fastq_pe_gz:
        output:
            # the wildcard name must be accession, pointing to an SRA number
            "data/pe/{accession}_1.fastq.gz",
            "data/pe/{accession}_2.fastq.gz",
        log:
            "logs/pe/{accession}.gz.log"
        params:
            extra="--skip-technical"
        threads: 6  # defaults to 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"


    rule get_fastq_pe_bz2:
        output:
            # the wildcard name must be accession, pointing to an SRA number
            "data/pe/{accession}_1.fastq.bz2",
            "data/pe/{accession}_2.fastq.bz2",
        log:
            "logs/pe/{accession}.bz2.log"
        params:
            extra="--skip-technical"
        threads: 6  # defaults to 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"


    rule get_fastq_se:
        output:
            "data/se/{accession}.fastq"
        log:
            "logs/se/{accession}.log"
        params:
            extra="--skip-technical"
        threads: 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"


    rule get_fastq_se_gz:
        output:
            "data/se/{accession}.fastq.gz"
        log:
            "logs/se/{accession}.gz.log"
        params:
            extra="--skip-technical"
        threads: 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"


    rule get_fastq_se_bz2:
        output:
            "data/se/{accession}.fastq.bz2"
        log:
            "logs/se/{accession}.bz2.log"
        params:
            extra="--skip-technical"
        threads: 6
        wrapper:
            "v3.0.1/bio/sra-tools/fasterq-dump"

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
-----

* The output format is automatically detected and, if needed, files compressed with either `gzip` or `bzip2`.
* Currently only supports PE samples
* The `extra` param alllows for additional program arguments.
* More information in, https://github.com/ncbi/sra-tools


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

* ``sra-tools=3.0.8``
* ``pigz=2.8``
* ``pbzip2=1.1.13``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Johannes Köster
* Derek Croote
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster, Derek Croote"
    __copyright__ = "Copyright 2020, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.snakemake import get_mem


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


    # Parse memory
    mem_mb = get_mem(snakemake, "MiB")


    # Outdir
    outdir = os.path.dirname(snakemake.output[0])
    if outdir:
        outdir = f"--outdir {outdir}"


    # Output compression
    compress = ""
    mem = f"-m{mem_mb}" if mem_mb else ""

    for output in snakemake.output:
        out_name, out_ext = os.path.splitext(output)
        if out_ext == ".gz":
            compress += f"pigz -p {snakemake.threads} {out_name}; "
        elif out_ext == ".bz2":
            compress += f"pbzip2 -p{snakemake.threads} {mem} {out_name}; "


    with tempfile.TemporaryDirectory() as tmpdir:
        mem = f"--mem {mem_mb}M" if mem_mb else ""

        shell(
            "(fasterq-dump --temp {tmpdir} --threads {snakemake.threads} {mem} "
            "{extra} {outdir} {snakemake.wildcards.accession}; "
            "{compress}"
            ") {log}"
        )


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