.. _`bio/fgbio/collectduplexseqmetrics`:

FGBIO COLLECTDUPLEXSEQMETRICS
=============================


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

Collects a suite of metrics to QC duplex sequencing data.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule CollectDuplexSeqMetrics:
        input:
            "mapped/{sample}.gu.bam"
        output:
            family_sizes="stats/{sample}.family_sizes.txt",
            duplex_family_sizes="stats/{sample}.duplex_family_sizes.txt",
            duplex_yield_metrics="stats/{sample}.duplex_yield_metrics.txt",
            umi_counts="stats/{sample}.umi_counts.txt",
            duplex_qc="stats/{sample}.duplex_qc.pdf",
            duplex_umi_counts="stats/{sample}.duplex_umi_counts.txt",
        params:
            extra=lambda wildcards: "-d " + wildcards.sample
        log:
            "logs/fgbio/collectduplexseqmetrics/{sample}.log"
        wrapper:
            "v3.0.1/bio/fgbio/collectduplexseqmetrics"

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


    from os import path
    from snakemake.shell import shell
    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[0]

    family_sizes = snakemake.output.family_sizes
    duplex_family_sizes = snakemake.output.duplex_family_sizes
    duplex_yield_metrics = snakemake.output.duplex_yield_metrics
    umi_counts = snakemake.output.umi_counts
    duplex_qc = snakemake.output.duplex_qc
    duplex_umi_counts = snakemake.output.get("duplex_umi_counts", None)

    file_path = str(path.dirname(family_sizes))
    name = str(path.basename(family_sizes)).split(".")[0]
    path_name_prefix = str(path.join(file_path, name))

    if not family_sizes == path_name_prefix + ".family_sizes.txt":
        raise Exception(
            "Unexpected family_sizes path/name format, expected {}, got {}.".format(
                path_name_prefix + ".family_sizes.txt", family_sizes
            )
        )
    if not duplex_family_sizes == path_name_prefix + ".duplex_family_sizes.txt":
        raise Exception(
            "Unexpected duplex_family_sizes path/name format, expected {}, got {}. Note that dirname will be extracted from family_sizes variable.".format(
                path_name_prefix + ".duplex_family_sizes.txt", duplex_family_sizes
            )
        )
    if not duplex_yield_metrics == path_name_prefix + ".duplex_yield_metrics.txt":
        raise Exception(
            "Unexpected duplex_yield_metrics path/name format, expected {}, got {}. Note that dirname will be extracted from family_sizes variable.".format(
                path_name_prefix + ".duplex_yield_metrics.txt", duplex_yield_metrics
            )
        )
    if not umi_counts == path_name_prefix + ".umi_counts.txt":
        raise Exception(
            "Unexpected umi_counts path/name format, expected {}, got {}. Note that dirname will be extracted from family_sizes variable.".format(
                path_name_prefix + ".umi_counts.txt", umi_counts
            )
        )
    if not duplex_qc == path_name_prefix + ".duplex_qc.pdf":
        raise Exception(
            "Unexpected duplex_qc path/name format, expected {}, got {}. Note that dirname will be extracted from family_sizes variable.".format(
                path_name_prefix + ".duplex_qc.pdf", duplex_qc
            )
        )
    if (
        duplex_umi_counts is not None
        and not duplex_umi_counts == path_name_prefix + ".duplex_umi_counts.txt"
    ):
        raise Exception(
            "Unexpected duplex_umi_counts path/name format, expected {}, got {}. Note that dirname will be extracted from family_sizes variable.".format(
                path_name_prefix + ".duplex_umi_counts.txt", duplex_umi_counts
            )
        )

    duplex_umi_counts_flag = ""
    if duplex_umi_counts is not None:
        duplex_umi_counts_flag = "-u "

    if not isinstance(bam_input, str) and len(snakemake.input) != 1:
        raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")

    shell(
        "fgbio {java_opts} CollectDuplexSeqMetrics"
        " -i {bam_input}"
        " -o {path_name_prefix}"
        " {duplex_umi_counts_flag}"
        " {extra_params}"
        " {log}"
    )


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