CUTADAPT-PE¶
Trim paired-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}.1.fastq", "reads/{sample}.2.fastq"]
output:
fastq1="trimmed/{sample}.1.fastq",
fastq2="trimmed/{sample}.2.fastq",
qc="trimmed/{sample}.qc.txt"
params:
# https://cutadapt.readthedocs.io/en/stable/guide.html#adapter-types
adapters_r1 = "-a AGAGCACACGTCTGAACTCCAGTCAC -g AGATCGGAAGAGCACACGT",
adapters_r2 = "-A AGAGCACACGTCTGAACTCCAGTCAC -G AGATCGGAAGAGCACACGT",
# https://cutadapt.readthedocs.io/en/stable/guide.html#
others = "--minimum-length 1 -q 20"
log:
"logs/cutadapt/{sample}.log"
wrapper:
"0.38.0/bio/cutadapt/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¶
- Julian de Ruiter
- David Laehnemann
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
n = len(snakemake.input)
assert n == 2, "Input must contain 2 (paired-end) elements."
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"cutadapt"
" {snakemake.params.adapters_r1}"
" {snakemake.params.adapters_r2}"
" {snakemake.params.others}"
" -o {snakemake.output.fastq1}"
" -p {snakemake.output.fastq2}"
" -j {snakemake.threads}"
" {snakemake.input}"
" > {snakemake.output.qc} {log}")