PURGE_DUPS CALCUTS

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/purge_dups/calcuts?label=version%20update%20pull%20requests

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:
        "v3.4.0-25-g0e80586/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

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)


shell("calcuts {extra} {snakemake.input[0]} > {snakemake.output[0]} {log}")