SICKLE SE

Trim single-end reads with sickle.

Software dependencies

  • sickle-trim ==1.33

Example

This wrapper can be used in the following way:

rule sickle_pe:
  input:
    "input_R1.fq"
  output:
    "output_R1.fq"
  params:
    qual_type="sanger",
    # optional extra parameters
    extra=""
  log:
    "logs/sickle/job.log"
  wrapper:
    "0.19.4/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 se -f {snakemake.input[0]} -o {snakemake.output[0]} "
    "-t {snakemake.params.qual_type} {extra}) {log}"
)