PICARD BEDTOINTERVALLIST

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

picard BedToIntervalList converts a BED file to Picard Interval List format.

Example

This wrapper can be used in the following way:

rule bed_to_interval_list:
    input:
        bed="resources/a.bed",
        dict="resources/genome.dict",
    output:
        "a.interval_list",
    log:
        "logs/picard/bedtointervallist/a.log",
    params:
        # optional parameters
        extra="--SORT true",  # sort output interval list before writing
    # optional specification of memory usage of the JVM that snakemake will respect with global
    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
    resources:
        mem_mb=1024,
    wrapper:
        "v3.8.0-1-g149ef14/bio/picard/bedtointervallist"

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

Software dependencies

  • picard=3.1.1

  • snakemake-wrapper-utils=0.6.2

Input/Output

Input:

Output:

  • interval_list Picard format

Authors

  • Fabian Kilpert

Code

__author__ = "Fabian Kilpert"
__copyright__ = "Copyright 2020, Fabian Kilpert"
__email__ = "fkilpert@gmail.com"
__license__ = "MIT"

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

log = snakemake.log_fmt_shell()

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

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "picard BedToIntervalList"
        " {java_opts} {extra}"
        " --INPUT {snakemake.input.bed}"
        " --SEQUENCE_DICTIONARY {snakemake.input.dict}"
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {snakemake.output}"
        " {log}"
    )