PURGE_DUPS

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:
    input:
        paf="split.self.paf.gz",
        #cov="pbcstat.cov",
        #cutoff="calcuts.cutoffs",
    output:
        "out/purge_dups.bed",
    log:
        "logs/purge_dups.log",
    params:
        extra="-2",
    threads: 1
    wrapper:
        "v3.8.0-40-ga41c0a0/bio/purge_dups/purge_dups"

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:

• Self-aligned split assembly in PAF format

Output:

• BED file

Authors

• Filipe Vieira

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)


cov = snakemake.input.get("cov", "")
if cov:
    cov = f"-c {cov}"

cutoff = snakemake.input.get("cutoff", "")
if cutoff:
    cutoff = f"-T {cutoff}"


shell(
    "purge_dups {cov} {cutoff} {extra} {snakemake.input.paf} > {snakemake.output[0]} {log}"
)