README.md

Metagenomic assembly nextflow pipeline

Usage

Usage:
    nextflow run main.nf

Options:
    --manifest                   Manifest containing paths to fastq files with headers ID,R1,R2. (mandatory)
    --skip_qc                    Skip metawrap qc step. [default: false] (optional)
    --keep_allbins               Keep allbins option for bin refinement.. [default: false] (optional)
    --keep_assembly              Don't cleanup assembly files. [default: false] (optional)
    --keep_binning               Don't cleanup binning files. [default: false] (optional)
    --keep_bin_refinement        Don't cleanup bin refinement files. [default: false] (optional)
    --keep_reassembly            Don't cleanup reassembly files. [default: false] (optional)
    --keep_metawrap_qc           Don't cleanup metawrap qc files. [default: false] (optional)
    --skip_reassembly            Skip reassembly step. [default: false] (optional)
    --fastspades                 Use fastspades assembly option. [default: false] (optional)
    --help                       Print this help message. (optional)

Generating manifests

If your data is stored in the PaM informatics pipeline system, you can use the following method:

./generate_manifest_from_lanes.sh -l <lanes_file>

For more information, run: ./generate_manifest_from_lanes.sh -h

If your data is not stored in the PaM informatics pipeline system, use the following method:

Step 1:

Obtain fastq paths: ls -d -1 <path>/*.fastq.gz > fastq_paths.txt

Step 2:

Generate manifest: ./generate_manifest.sh fastq_paths.txt

This will output the manifest to manifest.csv which can be fed into the nextflow pipeline

Dependencies

This pipeline relies on the following modules:

ISG/singularity/3.6.4
nextflow/22.10.6-5843