JELLYFISH_MERGE

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

Merge jellyfish databases.

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

Example

This wrapper can be used in the following way:

rule jellyfish_merge:
    input:
        "a.jf",
        "b.jf",
    output:
        "ab.jf",
    log:
        "ab.jf.log",
    wrapper:
        "v1.20.0-15-g28df43c2/bio/jellyfish/merge"

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:

  • multiple jf kmer count files

Output:

  • merged jf kmer count 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=True, stderr=True)


shell("(jellyfish merge {extra} -o {snakemake.output} {snakemake.input}) {log}")