nxf-fastqc

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

nextflow run angelovangel/nxf-fastqc --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 (example report). Some more detailed fastq file statistics are provided in an additional html report, using the faster and fastkmers programs (example Illumina, example Nanopore).

For all available pipeline options, try

nextflow run angelovangel/nxf-fastqc --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/nxf-fastqc --readsdir path/to/fastqfiles/ -profile conda

To run it with the included small test dataset

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

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