A generic pipeline for trimming, filtering, and dehosting reads that can be run on an arbitrary set of FASTQ files from Illumina or Nanopore NGS.
conda activate basic-sequence-trimmer
nextflow run <path/to/basic-sequence-trimmer> \
--label <label> \
--sheet <path/to/samplesheet> \
--outdir <output directory>
The output file structure is determined by the outdir:
<outdir>
├── pipeline_info
│ └── software_versions.yml
└── <label>
├── samplesheet.csv
└── fastq
└── [prefix_]<ID>.fastq[.gz]