.. _`bio/rbt/collapse_reads_to_fragments-bam`:

RBT COLLAPSE-READS-TO-FRAGMENTS BAM
===================================


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

Calculate consensus reads from read groups marked by PicardTools MarkDuplicates or UmiAwareMarkDuplicatesWithMateCigar.


**URL**: https://github.com/rust-bio/rust-bio-tools

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule calc_consensus_reads:
        input:
            "mapped/{sample}.marked.bam",
        output:
            consensus_r1="results/consensus/{sample}.1.fq",
            consensus_r2="results/consensus/{sample}.2.fq",
            consensus_se="results/consensus/{sample}.se.fq",
            skipped="results/consensus/{sample}.skipped.bam",
        params:
            extra="--annotate-record-ids",
        log:
            "logs/consensus/{sample}.log",
        wrapper:
            "v3.0.1/bio/rbt/collapse_reads_to_fragments-bam"

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

* ``rust-bio-tools=0.42.0``




Authors
-------

* Felix Mölder


Code
----

.. code-block:: python

    __author__ = "Felix Mölder"
    __copyright__ = "Copyright 2022, Felix Mölder"
    __email__ = "felix.moelder@uk-essen.de"
    __license__ = "MIT"

    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

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

    shell(
        "rbt collapse-reads-to-fragments bam {extra} {snakemake.input[0]} {snakemake.output} {log}"
    )


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