BEDGRAPHTOBIGWIG

Convert *.bedGraph file to *.bw file (see http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt)

Software dependencies

  • ucsc-bedgraphtobigwig == 377

Example

This wrapper can be used in the following way:

rule bedGraphToBigWig:
    input:
        bedGraph="{sample}.bedGraph",
        chromsizes="genome.chrom.sizes"
    output:
        "{sample}.bw"
    params:
        "" # optional params string
    wrapper:
        "0.56.0/bio/ucsc/bedGraphToBigWig"

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.

Authors

  • Roman Cherniatchik

Code

"""Snakemake wrapper for *.bedGraph to *.bw conversion using UCSC bedGraphToBigWig tool."""
# http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt

__author__ = "Roman Chernyatchik"
__copyright__ = "Copyright (c) 2019 JetBrains"
__email__ = "roman.chernyatchik@jetbrains.com"
__license__ = "MIT"

from snakemake.shell import shell

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

shell(
    "bedGraphToBigWig {extra}"
    " {snakemake.input.bedGraph} {snakemake.input.chromsizes}"
    " {snakemake.output} {log}"
)