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:
        "v1.31.1/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}"
)