CUTADAPT-SE¶
Trim single-end reads using cutadapt.
Software dependencies¶
- cutadapt ==2.5
- pigz ==2.3.4
Example¶
This wrapper can be used in the following way:
rule cutadapt:
input:
"reads/{sample}.fastq"
output:
fastq="trimmed/{sample}.fastq",
qc="trimmed/{sample}.qc.txt"
params:
"-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20"
log:
"logs/cutadapt/{sample}.log"
threads: 4 # set desired number of threads here
wrapper:
"0.50.1/bio/cutadapt/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.
Authors¶
- Julian de Ruiter
Code¶
"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"cutadapt"
" {snakemake.params}"
" -j {snakemake.threads}"
" -o {snakemake.output.fastq}"
" {snakemake.input[0]}"
" > {snakemake.output.qc} {log}"
)