PICARD CREATESEQUENCEDICTIONARY¶
Create a .dict file for a given FASTA file
URL:
Example¶
This wrapper can be used in the following way:
rule create_dict:
input:
"genome.fasta"
output:
"genome.dict"
log:
"logs/picard/create_dict.log"
params:
extra="" # optional: extra arguments for picard.
# 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:
"0.85.0/bio/picard/createsequencedictionary"
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.
Software dependencies¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
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=False, stderr=True)
shell(
"picard "
"CreateSequenceDictionary "
"{java_opts} {extra} "
"R={snakemake.input[0]} "
"O={snakemake.output[0]} "
"{log}"
)