nxf-fastqc

A simple fastp-MultiQC pipeline, written in nextflow. For a bunch of fastq files in a directory (Illumina PE or SE, Nanopore), run it with:

nextflow run angelovangel/nextflow-fastp --readsdir path/to/fastqfiles/

For Nanopore reads, add -profile ont to the command.

The pipeline executes fastp, saves the filtered files in results-fastp/fastp_trimmed, and generates a MultiQC report. That's it!

For all available options, try

nextflow run angelovangel/nextflow-fastp --help

If you have conda or docker, you can run the pipeline in a conda environment or in a docker container. Just add -profile conda or -profile docker to the nextflow command:

nextflow run angelovangel/nextflow-fastp --readsdir path/to/fastqfiles/ -profile conda

To run it with the included small test dataset

nextflow run angelovangel/nextflow-fastp -profile test 
# or combine profiles, e.g. -profile test,docker

If you don't have nextflow, go get it!