CLUSTALO¶
Multiple alignment of nucleic acid and protein sequences.
Example¶
This wrapper can be used in the following way:
rule clustalo:
input:
"{sample}.fa"
output:
"{sample}.msa.fa"
params:
extra=""
log:
"logs/clustalo/test/{sample}.log"
threads: 8
wrapper:
"v2.6.0/bio/clustalo"
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¶
clustalo=1.2.4
Authors¶
- Michael Hall
Code¶
"""Snakemake wrapper for clustal omega."""
__author__ = "Michael Hall"
__copyright__ = "Copyright 2019, Michael Hall"
__email__ = "mbhall88@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")
# Formats the log redrection string
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
# Executed shell command
shell(
"clustalo {extra}"
" --threads={snakemake.threads}"
" --in {snakemake.input[0]}"
" --out {snakemake.output[0]} "
" {log}"
)