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