PURGE_DUPS NGSCSTAT
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_ngscstat:
input:
bam="reads.bam",
output:
cov="out/ngscstat.cov",
stat="out/ngscstat.stat",
log:
"logs/ngscstat.log",
params:
extra="",
threads: 1
wrapper:
"v5.0.1/bio/purge_dups/ngscstat"
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:
mapped reads in PAF format
Output:
coverage
stats
Code
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2022, Filipe G. Vieira"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell("ngscstat {extra} -O {tmpdir} {snakemake.input} {log}")
if snakemake.output.get("cov"):
shell("cat {tmpdir}/TX.base.cov > {snakemake.output.cov}")
if snakemake.output.get("stat"):
shell("cat {tmpdir}/TX.stat > {snakemake.output.stat}")