.. _`bio/cnv_facets`:

CNV_FACETS
==========


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

cnv_facets detects somatic copy number variants (CNVs)


**URL**: https://github.com/dariober/cnv_facets

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_cnv_facets_bam:
        input:
            tumor="T.sample.bam",
            normal="N.sample.bam",
            vcf="common.sample.vcf.gz",
        output:
            vcf="CNV_bam.vcf.gz",
            cnv="genome_bam.cnv.png",
            hist="cnv_bam.hist.pdf",
            spider="qc_bam.spider.pdf",
        log:
            "logs/cnv_facets_bam.log",
        params:
            extra="",
        wrapper:
            "v3.3.2/bio/cnv_facets"


    rule test_cnv_facets_pileup:
        input:
            pileup="pileup.csv.gz",
            vcf="common.sample.vcf.gz",
        output:
            vcf="CNV_pileup.vcf.gz",
            cnv="genome_pileup.cnv.png",
            hist="cnv_pileup.hist.pdf",
            spider="qc_pileup.spider.pdf",
        log:
            "logs/cnv_facets_bam.log",
        params:
            extra="",
        wrapper:
            "v3.3.2/bio/cnv_facets"

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

* ``cnv_facets=0.16.0``
* ``python=3.8.15``

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

* ``tumor``: Path to tumor aligned reads. (BAM, required if `pileup` is empty)
* ``normal``: Path to normal aligned reads. (BAM, required if `pileup` is empty)
* ``vcf``: Path to common, polymorphic SNPs. (pbgzip VCF)
* ``pileup``: Path to pileup variants. (pbgzip CSV, replaces `tumor` and `normal`)

**Output:**

* ``vcf``: Path to copy number variants. (pbgzip VCF)
* ``cnv``: Path to a summary plot of CNVs across the genome. (PNG)
* ``hist``: Path to histograms of the distribution of read depth across all the position in the tumour and normal sample, before and after filtering positions. (PDF)
* ``spider``: Path to a diagnostic plot to check how well the copy number fits work (PDF)



Params
------

* ``extra``: Optional parameters given to `cnv_facets`, besides `-t`, `-n`, `-vcf` and `-o`.




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # coding: utf-8

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2023, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    from snakemake.shell import shell
    from tempfile import TemporaryDirectory

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

    # Consider user input datasets
    input_data = ""
    if all(key in snakemake.input.keys() for key in ["tumor", "normal"]):
        input_data = f" --snp-tumour {snakemake.input.tumor} --snp-normal {snakemake.input.normal}  --snp-vcf {snakemake.input.vcf} "
    elif "pileup" in snakemake.input.keys():
        input_data = f" --pileup {snakemake.input.pileup} --snp-vcf {snakemake.input.vcf} "
    else:
        raise KeyError(
            "Either provide both `tumor` *and* `normal` bam files, "
            "or a unique `pileup` file."
        )

    with TemporaryDirectory() as tempdir:
        prefix = f"{tempdir}/facets_output"

        # Run cnv_facets
        shell(
            "cnv_facets.R "
            "{extra} "
            "--snp-nprocs {snakemake.threads} "
            "{input_data} "
            "-o {prefix} "
            "{log}"
        )

        # Allow user to define all output files
        if snakemake.output.get("vcf"):
            shell("mv --verbose {prefix}.vcf.gz {snakemake.output.vcf} {log}")
            shell("mv --verbose {prefix}.vcf.gz.tbi {snakemake.output.vcf}.tbi {log}")

        if snakemake.output.get("cnv"):
            shell("mv --verbose {prefix}.cnv.png {snakemake.output.cnv} {log}")

        if snakemake.output.get("hist"):
            shell("mv --verbose {prefix}.cov.pdf {snakemake.output.hist} {log}")

        if snakemake.output.get("spider"):
            shell("mv --verbose {prefix}.spider.pdf {snakemake.output.spider} {log}")


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