Convenient workflow for wastewater COVID-19 report generation on Variants of Concern (VOCs) powered by NextFlow, Conda and Singularity

• Nextflow >=20.07.1 (for DSL 2 support)
• Singularity
• Conda
• Git LFS (optional)

1. Create nextflow conda environment with latest NextFlow installed

     conda create -n nextflow@latest nextflow && conda activate nextflow@latest

2. Install git-lfs to download Singularity image to data folder

       # if running inside conda environment
       conda install -c conda-forge git-lfs
       # if running locally on Ubuntu
       apt-get install git-lfs
   

3. Clone repository with Git and Git LFS

       git clone https://github.com/justinschonfeldc/nfwwreporting.git
       git lfs pull
   

4. Run NextFlow on inputs (see Running and Usage sections)

Note: Singularity is already installed on the waffles server, but NextFlow conda environment is outdated. We recommend installating custom NextFlow conda environment

1. Activate NextFlow Conda environment if NextFlow run from Conda

   conda activate -n nextflow@latest
   
   

2. Setup inputs and run NextFlow workflow. Additional run parameters are in the Usage section

   nextflow run main.nf -profile conda --resume

Pipeline that automates COVID-19 wastewater report generation
    Usage:
    nextflow run --consensus_file consensus.fasta --bam_file consensus.bam  -profile <profile>
    Mandatory arguments:
      --consensus_file [file]                   Path to the consensus COVID-19 genome wastewater assembly
      --bam_file [file]                         Path to the aligned wastewater reads to the MN908947.3 reference
      --vcfparser_batch_file                    Path to VCFParser input batch file with sample name, abs path to TSV/VCF file and BAM file
      -profile                                  Available: conda, singularity, standard
      --resume                                  Resume from the last failed step
      --help                                    Display this help message

Sample BAM File

Sample Consensus FIle

IVAR Output File

GISAID Metadata

GISAID Multiple Sequence Alignment

Variant Specification