SICKLE SE
Trim single-end reads with sickle.
Example
This wrapper can be used in the following way:
rule sickle_se:
input:
"reads/{sample}.1.fastq"
output:
"{sample}.1.fastq"
log:
"logs/sickle/{sample}.log"
params:
qual_type="sanger",
# optional extra parameters
extra=""
wrapper:
"v5.8.0-3-g915ba34/bio/sickle/se"
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 se -f {snakemake.input[0]} -o {snakemake.output[0]} "
"-t {snakemake.params.qual_type} {extra}) {log}"
)