This is a modular Snakemake workflow for various repeat masking tools.
from snakemake.utils import min_version
min_version("6.0")
# define your configuration via python
# or define a yaml e.g.
# configfile: "config/config.yaml"
config = {
"samples": {
"test": ".test/test.fa.gz",
"test2": ".test/test.fa.gz",
}
}
module Rhodonite:
snakefile:
"https://github.com/mrvollger/Rhodonite/raw/master/workflow/Snakefile"
config:
config
# import the rules from Rhodonite
use rule * from Rhodonite as Rhodonite_*
# use RepeatMasker rules from Rhodonite
use rule RepeatMasker from Rhodonite as Rhodonite_RepeatMasker with:
output:
# You rename the output to anything you want
# but maintain the order and keep "{sample}" in the name and the (.gz).
# Every rule will have the standard output of the program
# and a bed output that is sorted in the order of the ref.
out="{sample}.rm.out",
bed="{sample}.rm.bed.gz",
# use trf rules from Rhodonite
use rule trf from Rhodonite as Rhodonite_trf with:
output:
dat="{sample}.trf.dat",
bed="{sample}.trf.bed.gz",
# use DupMasker rules from Rhodonite
use rule DupMasker from Rhodonite as Rhodonite_DupMasker with:
output:
extra="{sample}.duplicons.extra",
bed="{sample}.duplicons.bed.gz",
rule all:
input:
expand(rules.Rhodonite_RepeatMasker.output, sample=config["samples"].keys()),
expand(rules.Rhodonite_trf.output, sample=config["samples"].keys()),
expand(rules.Rhodonite_DupMasker.output, sample=config["samples"].keys()),For a complete documented example see examples/example.smk.