BGZIP

Block compression/decompression utility

URL: https://github.com/samtools/htslib

Example

This wrapper can be used in the following way:

rule bgzip:
    input:
        "{prefix}.vcf",
    output:
        "{prefix}.vcf.gz",
    params:
        extra="", # optional
    threads: 1
    log:
        "logs/bgzip/{prefix}.log",
    wrapper:
        "v9.4.1/bio/bgzip"

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

• Run mode (compression/decompression) is automatically inferred from the extension of the input file.

Software dependencies

• htslib=1.23.1

Input/Output

Input:

• file to be compressed or decompressed

Output:

• compressed or decompressed output

Params

• extra: additional bgzip parameters

Authors

• William Rowell

• Filipe G. Vieira

Code

__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"


from snakemake.shell import shell

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


if snakemake.input[0].endswith(".gz"):
    extra += " --decompress"


shell(
    "bgzip --threads {snakemake.threads} {extra} --output {snakemake.output[0]} {snakemake.input[0]} {log}"
)