JELLYFISH_DUMP

Dump kmers from jellyfish database

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

Example

This wrapper can be used in the following way:

rule jellyfish_dump:
    input:
        "{prefix}.jf",
    output:
        "{prefix}.dump",
    log:
        "{prefix}.log",
    params:
        extra="-c -t",
    wrapper:
        "v1.25.0-52-g79342b73/bio/jellyfish/dump"

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:

• dump of kmer counts

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 dump {extra} -o {snakemake.output} {snakemake.input}) {log}")