.. _`bio/fgbio/annotatebamwithumis`:

FGBIO ANNOTATEBAMWITHUMIS
=========================


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

Annotates existing BAM files with UMIs (Unique Molecular Indices, aka Molecular IDs, Molecular barcodes) from a separate FASTQ file.

**URL**: https://fulcrumgenomics.github.io/fgbio/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule annotate_bam_single_fastq:
        input:
            bam="mapped/{sample}.bam",
            umi="umi/{sample}.fastq",
        output:
            "mapped/{sample}.annotated.bam",
        params:
            "",
        resources:
            # suggestion assuming unsorted input, so that memory should
            # be proportional to input size:
            # https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
            mem_mb=lambda wildcards, input: max([input.size_mb * 1.3, 200]),
        log:
            "logs/fgbio/annotate_bam/{sample}.log",
        wrapper:
            "v3.0.4/bio/fgbio/annotatebamwithumis"


    rule annotate_bam_multiple_fastqs:
        input:
            bam="mapped/{sample}.bam",
            umi=[
                "umi/{sample}.fastq",
                "umi/{sample}.fastq",
            ],
        output:
            "mapped/{sample}-{sample}.annotated.bam",
        params:
            "",
        resources:
            # suggestion assuming unsorted input, so that memory should
            # be proportional to input size:
            # https://fulcrumgenomics.github.io/fgbio/tools/latest/AnnotateBamWithUmis.html
            mem_mb=lambda wildcards, input: max([input.size_mb * 1.3, 200]),
        log:
            "logs/fgbio/annotate_bam/{sample}-{sample}.log",
        wrapper:
            "v3.0.4/bio/fgbio/annotatebamwithumis"

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
---------------------

* ``fgbio=2.1.0``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2018, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake.io import Namedlist
    from snakemake_wrapper_utils.java import get_java_opts

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra_params = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    bam_input = snakemake.input.bam

    if bam_input is None:
        raise ValueError("Missing bam input file!")
    elif not isinstance(bam_input, str):
        raise ValueError("Input bam should be a string: " + str(bam_input) + "!")

    umi_input = snakemake.input.umi

    if umi_input is None:
        raise ValueError("Missing input file with UMIs")
    elif not (isinstance(umi_input, str) or isinstance(umi_input, Namedlist)):
        raise ValueError(
            "Input UMIs-file should be a string or a snakemake io list: "
            + str(umi_input)
            + "!"
        )

    if not len(snakemake.output) == 1:
        raise ValueError("Only one output value expected: " + str(snakemake.output) + "!")
    output_file = snakemake.output[0]


    if output_file is None:
        raise ValueError("Missing output file!")
    elif not isinstance(output_file, str):
        raise ValueError("Output bam-file should be a string: " + str(output_file) + "!")

    shell(
        "fgbio {java_opts} AnnotateBamWithUmis"
        " -i {bam_input}"
        " -f {umi_input}"
        " -o {output_file}"
        " {extra_params}"
        " {log}"
    )


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