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:
    "v3.8.0-49-g6f33607/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

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}"
)