PICARD CREATESEQUENCEDICTIONARY¶
Create a .dict file for a given FASTA file
Software dependencies¶
- picard ==2.9.2
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.
wrapper:
"0.33.0/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.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
'picard '
'CreateSequenceDictionary '
'{extra} '
'R={snakemake.input[0]} '
'O={snakemake.output[0]} '
'{log}')