MetaFlow

A Nextflow workflow to process short-read metagenome data. The workflow includes the following steps:

1. QC: fastp and fastQC
2. Assembly: MEGAHIT and metaQUAST
3. Annotation: prokka
4. Taxonomic assignment: metaphlan

Notes:

• 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

Setup:

1. Clone repository
2. Install Nextflow
3. Install Singularity or Docker
4. Create 'data' folder in main directory and change relevant paths in the config file (lines 13 and 24)

To run:

nextflow run WGS.nf --in_dir directory/with/fastq/files -profile (docker OR singularity)

Workflow can be tested with:

nextflow run WGS.nf --in_dir test_reads -profile (docker OR singularity)

SLURM submission:

sbatch example_sbatch_script.sh