.. _`bio/picard/collectalignmentsummarymetrics`:

PICARD COLLECTALIGNMENTSUMMARYMETRICS
=====================================


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

Collect metrics on aligned reads with picard tools.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule alignment_summary:
        input:
            ref="genome.fasta",
            bam="mapped/{sample}.bam",
        output:
            "stats/{sample}.summary.txt",
        log:
            "logs/picard/alignment-summary/{sample}.log",
        params:
            # optional parameters (e.g. relax checks as below)
            extra="--VALIDATION_STRINGENCY LENIENT --METRIC_ACCUMULATION_LEVEL null --METRIC_ACCUMULATION_LEVEL SAMPLE",
        # optional specification of memory usage of the JVM that snakemake will respect with global
        # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
        # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
        # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/picard/collectalignmentsummarymetrics"

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`
* For more information see, https://broadinstitute.github.io/picard/command-line-overview.html#CollectAlignmentSummaryMetrics


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

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




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com"
    __license__ = "MIT"


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

    log = snakemake.log_fmt_shell()

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "picard CollectAlignmentSummaryMetrics"
            " {java_opts} {extra}"
            " --INPUT {snakemake.input.bam}"
            " --REFERENCE_SEQUENCE {snakemake.input.ref}"
            " --TMP_DIR {tmpdir}"
            " --OUTPUT {snakemake.output[0]}"
            " {log}"
        )


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