A Nextflow workflow to process short-read metagenome data. The workflow includes the following steps:
- QC: fastp and fastQC
- Assembly: MEGAHIT and metaQUAST
- Annotation: prokka
- Taxonomic assignment: metaphlan
- The workflow is configured to work with docker or singularity. The singularity profile works with SLURM by default, an sbatch job can be submitted with the available example script.
- Fastq files must be named *_L001_R{1,2}_001.fastq.gz
- Clone repository
- Install Nextflow
- Install Singularity or Docker
- Create 'data' folder in main directory and change relevant paths in the config file (lines 13 and 24)
nextflow run WGS.nf --in_dir directory/with/fastq/files -profile (docker OR singularity)
nextflow run WGS.nf --in_dir test_reads -profile (docker OR singularity)
sbatch example_sbatch_script.sh