.. _`bio/benchmark/chm-eval-sample`:

CHM-EVAL-SAMPLE
===============


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

Download CHM-eval sample for benchmarking variant calling.

**URL**: https://github.com/lh3/CHM-eval

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule chm_eval_sample:
        output:
            bam="resources/chm-eval-sample.bam",
            bai="resources/chm-eval-sample.bam.bai"
        params:
            # Optionally only grab the first 100 records.
            # This is for testing, remove next line to grab all records.
            first_n=100
        log:
            "logs/chm-eval-sample.log"
        wrapper:
            "v3.0.1/bio/benchmark/chm-eval-sample"

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

* ``samtools=1.18``
* ``curl``



Params
------

* ``first_n``: Optional parameter for grab only the first `n` elements.




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2020, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    url = "ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR134/ERR1341796/CHM1_CHM13_2.bam"

    pipefail = ""
    fmt = "-b"
    prefix = snakemake.params.get("first_n", "")
    if prefix:
        prefix = "| head -n {} | samtools view -h -b".format(prefix)
        fmt = "-h"
        pipefail = "set +o pipefail"

        shell(
            """
            {pipefail}
            {{
                samtools view {fmt} {url} {prefix} > {snakemake.output.bam}
                samtools index {snakemake.output.bam}
            }} {log}
            """
        )
    else:
        shell(
            """
            {{
                curl -L {url} > {snakemake.output.bam}
                samtools index {snakemake.output.bam}
            }} {log}
            """
        )


.. |nl| raw:: html

   <br>