GATK INTERVALLISTTOBED

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Run gatk IntervalListToBed.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570392740123-IntervalListToBed-Picard-

Example

This wrapper can be used in the following way:

rule gatk_interval_list_to_bed:
    input:
        intervals="genome.intervals",
    output:
        bed="genome.bed",
    log:
        "logs/genome.log",
    params:
        extra="",
        java_opts="",  # optional
    resources:
        mem_mb=1024,
    wrapper:
        "v3.9.0/bio/gatk/intervallisttobed"

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 java_opts param allows for additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).

  • The extra param allows for additional program arguments.

Software dependencies

  • gatk4=4.5.0.0

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

  • interval list

Output:

  • bed file

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2021, Filipe G. Vieira"
__license__ = "MIT"

import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)


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

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' IntervalListToBed"
        " --INPUT {snakemake.input.intervals}"
        " {extra}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output.bed}"
        " {log}"
    )