BUSCO

Assess assembly and annotation completeness with BUSCO

Software dependencies

• busco ==3.0.2

Example

This wrapper can be used in the following way:

rule run_busco:
    input:
        "transcriptome.fasta"
    output:
        "run_txome_busco/full_table_txome_busco.tsv",
    log:
        "logs/quality/transcriptome_busco.log"
    threads: 8
    params:
        mode="transcriptome",
        lineage_path="metazoa_test",
        # optional parameters
        extra=""
    wrapper:
        "0.27.0/bio/busco"

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

• Tessa Pierce

Code

"""Snakemake wrapper for Salmon Index."""

__author__ = "Tessa Pierce"
__copyright__ = "Copyright 2018, Tessa Pierce"
__email__ = "ntpierce@gmail.com"
__license__ = "MIT"

from snakemake.shell import shell
from os import path

log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
mode = snakemake.params.get("mode")
assert mode is not None, "please input a run mode: genome, transcriptome or proteins"
lineage = snakemake.params.get("lineage_path")
assert lineage is not None, "please input the path to a lineage for busco assessment"

out_name = path.dirname(snakemake.output[0])
assert '/' not in out_name, "out name cannot be path"
assert out_name.startswith('run_'), " out name must start with run_"
out_name = out_name.split('run_')[1] # busco adds "run_" automatically

#note: --force allows snakemake to handle rewriting files as necessary
# without needing to specify *all* busco outputs as snakemake outputs
shell("run_busco --in {snakemake.input} --out {out_name} --force "
      " --cpu {snakemake.threads} --mode {mode} --lineage {lineage} "
      " {extra} {log}" )