PURGE_DUPS SPLIT_FA

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_split_fa:
    input:
        "{a}.fasta",
    output:
        "out/{a}.split",
    log:
        "logs/{a}.split_fa.log",
    params:
        extra="",
    threads: 1
    wrapper:
        "v3.9.0/bio/purge_dups/split_fa"

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