CUTADAPT-PE¶
Trim paired-end reads using cutadapt.
URL:
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="-a AGAGCACACGTCTGAACTCCAGTCAC -g AGATCGGAAGAGCACACGT -A AGAGCACACGTCTGAACTCCAGTCAC -G AGATCGGAAGAGCACACGT",
# https://cutadapt.readthedocs.io/en/stable/guide.html#
extra="--minimum-length 1 -q 20"
log:
"logs/cutadapt/{sample}.log"
threads: 4 # set desired number of threads here
wrapper:
"0.80.1/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.
Software dependencies¶
cutadapt==3.4
Input/Output¶
Input:
- two (paired-end) fastq files
Output:
- two trimmed (paired-end) fastq files
- text file containing trimming statistics
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."
extra = snakemake.params.get("extra", "")
adapters = snakemake.params.get("adapters", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
assert (
extra != "" or adapters != ""
), "No options provided to cutadapt. Please use 'params: adapters=' or 'params: extra='."
shell(
"cutadapt"
" {adapters}"
" {extra}"
" -o {snakemake.output.fastq1}"
" -p {snakemake.output.fastq2}"
" -j {snakemake.threads}"
" {snakemake.input}"
" > {snakemake.output.qc} {log}"
)