PICARD BEDTOINTERVALLIST

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

Software dependencies

  • picard ==2.22.1

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
        "SORT=true " # sort output interval list before writing
    wrapper:
        "0.65.0/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.

Authors

  • Fabian Kilpert

Code

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


from snakemake.shell import shell


log = snakemake.log_fmt_shell()


shell(
    "picard BedToIntervalList "
    "{snakemake.params} "
    "INPUT={snakemake.input.bed} "
    "SEQUENCE_DICTIONARY={snakemake.input.dict} "
    "OUTPUT={snakemake.output} "
    "{log} "
)