JELLYFISH_MERGE#
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:
"v3.0.4-12-g561ccaf/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
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}")