SICKLE PE
Trim paired-end reads with sickle.
Example
This wrapper can be used in the following way:
rule sickle_pe:
input:
r1="reads/{sample}.1.fastq",
r2="reads/{sample}.2.fastq"
output:
r1="{sample}.1.fastq",
r2="{sample}.2.fastq",
rs="{sample}.single.fastq",
log:
"logs/sickle/{sample}.log"
params:
qual_type="sanger",
# optional extra parameters
extra=""
wrapper:
"v3.9.0/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.
Software dependencies
sickle-trim=1.33
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}"
)