MERYL STATS

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/meryl/stats?label=version%20update%20pull%20requests

A genomic k-mer counter (and sequence utility) with nice features.

URL: https://github.com/marbl/meryl

Example

This wrapper can be used in the following way:

rule meryl_stats:
    input:
        "{genome}",
    output:
        "{genome}.stats",
    log:
        "logs/meryl_stats/{genome}.log",
    params:
        command="statistics",
    wrapper:
        "v3.9.0-1-gc294552/bio/meryl/stats"

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.

Notes

  • The command param allows to specify which stats to print: statistics (display total, unique, distinct kmers) [default], histogram (display kmer frequency), or print (display kmers).

Software dependencies

  • meryl=2013

Input/Output

Input:

  • meryl database(s)

Output:

  • meryl stats (either the kmers, statistics, or histogram)

Authors

  • Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"


from snakemake.shell import shell


log = snakemake.log_fmt_shell(stdout=False, stderr=True)


command = snakemake.params.get("command", "statistics")
assert command in [
    "statistics",
    "histogram",
    "print",
], "invalid command specified."


shell("meryl {command} {snakemake.input} > {snakemake.output} {log}")