PURGE_DUPS CALCUTS
Purge haplotigs and overlaps in an assembly based on read depth
URL: https://github.com/dfguan/purge_dups
Example
This wrapper can be used in the following way:
rule purge_dups_calcuts:
input:
"pbcstat.stat",
output:
"out/calcuts.cutoffs",
log:
"logs/calcuts.log",
params:
extra="-l 2 -m 4 -u 8",
threads: 1
wrapper:
"v5.0.0/bio/purge_dups/calcuts"
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.
Notes
The extra param allows for additional program arguments.
Software dependencies
purge_dups=1.2.6
Input/Output
Input:
stats file
Output:
coverage cut-offs
Code
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("calcuts {extra} {snakemake.input[0]} > {snakemake.output[0]} {log}")