.. _`bio/umis/bamtag`:

UMIS BAMTAG
===========


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

Convert a BAM/SAM with fastqtransformed read names to have UMI and


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule umis_bamtag:
        input:
            "data/{sample}.bam"
        output:
            "data/{sample}.annotated.bam"
        log:
            "logs/umis/bamtag/{sample}.log"
        params:
            extra=""
        threads: 1
        wrapper:
            "v3.0.1/bio/umis/bamtag"

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

* ``umis=1.0.9``
* ``samtools=1.18``




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2019, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __license__ = "MIT"


    import os
    from snakemake.shell import shell

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

    bam_input = snakemake.input[0]

    if bam_input is None:
        raise ValueError("Missing bam input file!")
    elif not len(snakemake.input) == 1:
        raise ValueError("Only expecting one input file: " + str(snakemake.input) + "!")

    output_file = snakemake.output[0]

    if output_file is None:
        raise ValueError("Missing output file")
    elif not len(snakemake.output) == 1:
        raise ValueError("Only expecting one output file: " + str(output_file) + "!")

    in_pipe = ""
    if bam_input.endswith(".sam"):
        in_pipe = "cat "
    else:
        in_pipe = "samtools view -h "

    out_pipe = ""
    if not output_file.endswith(".sam"):
        out_pipe = " | samtools view -S -b - "

    shell(
        " {in_pipe} {bam_input} | " " umis bamtag -" " {out_pipe} > {output_file}" " {log}"
    )


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