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} "
)