BCFTOOLS SORT

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/bcftools/sort?label=version%20update%20pull%20requests

Sort vcf/bcf file.

URL: http://www.htslib.org/doc/bcftools.html#sort

Example

This wrapper can be used in the following way:

rule bcftools_sort:
    input:
        "{sample}.bcf",
    output:
        "{sample}.sorted.bcf",
    log:
        "logs/bcftools/sort/{sample}.log",
    params:
        # Set to True, in case you want uncompressed BCF output
        uncompressed_bcf=False,
        # Extra arguments
        extras="",
    resources:
        mem_mb=8000,
    wrapper:
        "v3.10.2/bio/bcftools/sort"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Notes

  • The uncompressed_bcf param allows to specify that a BCF output should be uncompressed (ignored otherwise).

  • The extra param allows for additional program arguments (not –threads, -o/–output, -O/–output-type, -m/–max-mem, or -T/–temp-dir).

Software dependencies

  • bcftools=1.20

  • snakemake-wrapper-utils=0.6.2

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2020, Filipe G. Vieira"
__license__ = "MIT"


import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts


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


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "bcftools sort"
        " {bcftools_opts}"
        " {extra}"
        " --temp-dir {tmpdir}"
        " {snakemake.input[0]}"
        " {log}"
    )