.. _`bio/biobambam2/bamsormadup`:

BIOBAMBAM2 BAMSORMADUP
======================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/biobambam2/bamsormadup?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/biobambam2/bamsormadup

Mark PCR and optical duplicates, followed with sorting, with BioBamBam2 tools.


**URL**: https://gitlab.com/german.tischler/biobambam2

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule mark_duplicates_bamsormadup:
        input:
            "mapped/{sample}.bam",
        output:
            bam="dedup/{sample}.bam",
            index="dedup/{sample}.bai",
            metrics="dedup/{sample}.metrics.txt",
        log:
            "logs/{sample}.log",
        params:
            extra="SO=coordinate",
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.4/bio/biobambam2/bamsormadup"

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

* ``biobambam=2.0.183``

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

* Path to SAM/BAM/CRAM file, this must be the first file in the input file list.
* Path to reference (for CRAM output)

**Output:**

* Path to SAM/BAM/CRAM file with marked duplicates. This must be the fist output file in the output file list.
* ``index``: Path to BAM index file (optional)
* ``metrics``: Path to metrics file (optional)



Params
------

* ``extra``: additional program arguments (not `inputformat`, `outputformat` or `tmpfile`).




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2021, Filipe G. Vieira"
    __license__ = "MIT"


    import os
    import random
    import tempfile
    from pathlib import Path
    from snakemake.shell import shell


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


    # File formats
    in_name, in_format = os.path.splitext(snakemake.input[0])
    in_format = in_format.lstrip(".")
    out_name, out_format = os.path.splitext(snakemake.output[0])
    out_format = out_format.lstrip(".")


    index = snakemake.output.get("index", "")
    if index:
        index = f"indexfilename={index}"


    metrics = snakemake.output.get("metrics", "")
    if metrics:
        metrics = f"M={metrics}"


    with tempfile.TemporaryDirectory() as tmpdir:
        # This folder must not exist; it is created by BamSorMaDup
        tmpdir_bamsormadup = Path(tmpdir) / "bamsormadup_{:06d}".format(
            random.randrange(10**6)
        )

        shell(
            "bamsormadup threads={snakemake.threads}"
            " inputformat={in_format}"
            " tmpfile={tmpdir_bamsormadup}"
            " outputformat={out_format}"
            " {index} {metrics} {extra}"
            " < {snakemake.input[0]} > {snakemake.output[0]}"
            " {log}"
        )


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