SICKLE PE¶
Trim paired-end reads with sickle.
Software dependencies¶
- sickle-trim ==1.33
Example¶
This wrapper can be used in the following way:
rule sickle_pe:
input:
r1="input_R1.fq",
r2="input_R2.fq"
output:
r1="output_R1.fq",
r2="output_R2.fq",
rs="output_single.fq",
params:
qual_type="sanger",
# optional extra parameters
extra=""
log:
# optional log file
"logs/sickle/job.log"
wrapper:
"0.33.0/bio/sickle/pe"
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.
Authors¶
- Wibowo Arindrarto
Code¶
__author__ = "Wibowo Arindrarto"
__copyright__ = "Copyright 2016, Wibowo Arindrarto"
__email__ = "bow@bow.web.id"
__license__ = "BSD"
from snakemake.shell import shell
# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell()
shell(
"(sickle pe -f {snakemake.input.r1} -r {snakemake.input.r2} "
"-o {snakemake.output.r1} -p {snakemake.output.r2} "
"-s {snakemake.output.rs} -t {snakemake.params.qual_type} "
"{extra}) {log}"
)