This is a simple docker/wolF tool for cutadapt to trim fastq/read sequences for adapters, low-quality, etc.

Docker

Current docker comes with pigz for parallel compression:

gcr.io/broad-getzlab-workflows/cutadapt:v3

Version:

# cutadapt --version
4.5

Please read the doc https://cutadapt.readthedocs.io/en/v4.5/guide.html to adjust wolF parameters.

Usage

import wolf
cutadapt = wolf.ImportTask("git@github.com:jalberge/cutadapt_TOOL.git")
trimmed_fastqs = cutadapt.cutadapt(inputs={"fastq1":fastqs["fastq1"], "fastq2":fastqs["fastq2"]})