.. _`bio/picard/collectrnaseqmetrics`:

PICARD COLLECTRNASEQMETRICS
===========================


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

Run picard CollectRnaSeqMetrics to generate QC metrics for RNA-seq data.


**URL**: https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule alignment_summary:
        input:
            # BAM aligned, splicing-aware, to reference genome
            bam="mapped/a.bam",
    	# Reference genome
            #ref="ref.fasta",
            # Annotation file containing transcript, gene, and exon data
            refflat="annotation.refFlat",
        output:
            "results/a.rnaseq_metrics.txt",
        params:
            # strand is optional (defaults to NONE) and pertains to the library preparation
            # options are FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND, and NONE
            strand="NONE",
            # optional additional parameters, for example,
            extra="--VALIDATION_STRINGENCY STRICT",
        log:
            "logs/picard/rnaseq-metrics/a.log",
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/picard/collectrnaseqmetrics"

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 `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
* The `extra` param allows for additional program arguments.
* `--TMP_DIR` is automatically set by `resources.tmpdir`


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

* ``picard=3.1.1``
* ``snakemake-wrapper-utils=0.6.2``

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

* BAM file of RNA-seq data aligned to genome
* REF_FLAT formatted file of transcriptome annotations
* reference FASTA (optional)

**Output:**

* RNA-Seq metrics text file




Authors
-------

* Brett Copeland
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Brett Copeland"
    __copyright__ = "Copyright 2021, Brett Copeland"
    __email__ = "brcopeland@ucsd.edu"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts

    log = snakemake.log_fmt_shell()

    strand = snakemake.params.get("strand", "NONE")
    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)


    ref = snakemake.input.get("ref", "")
    if ref:
        ref = f"--REFERENCE_SEQUENCE {ref}"


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "picard CollectRnaSeqMetrics"
            " {java_opts} {extra}"
            " --INPUT {snakemake.input.bam}"
            " {ref}"
            " --REF_FLAT {snakemake.input.refflat}"
            " --STRAND_SPECIFICITY {strand}"
            " --TMP_DIR {tmpdir}"
            " --OUTPUT {snakemake.output}"
            " {log}"
        )


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