JELLYFISH_HISTO

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

Export histogram of kmer counts.

URL: https://github.com/gmarcais/Jellyfish

Example

This wrapper can be used in the following way:

rule jellyfish_histo:
    input:
        "{prefix}.jf",
    output:
        "{prefix}.histo",
    log:
        "{prefix}.log",
    threads: 2
    wrapper:
        "v1.20.0-15-g28df43c2/bio/jellyfish/histo"

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

  • kmer-jellyfish=2.3.0

Input/Output

Input:

  • kmer count jf file

Output:

  • kmer histogram file

Authors

  • William Rowell

Code

__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"

from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)


shell(
    """
    (jellyfish histo \
        {extra} \
        --threads={snakemake.threads} \
        {snakemake.input} > {snakemake.output}) {log}
    """
)