A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

Table of contents -

• Version updates
• Pipeline Diagram
• Requirements
• Quick start guide
  • parameters setup
  • Test Data
  • Run on local server
  • Requirements
  • Illumina pipeline
  • Nanopore nanopolish pipeline
  • Nanopore medaka pipeline
  • How to run in NGP server
  • Datafile structure
  • Pipeline run command
    • Illumina pipeline
    • Nanopore pipeline

• Useful information

  Version updates

  v2.0.0

  Major updates

• Docker container separated for Pangolin typing
  • Illumina container: gms-artic-illumina
  • Nanopore container: gms-artic-nanopore
  • Pangolin container: gms-artic-pangolin
  • pycoQC container : pycoqc
• Added separate package version files for each workflow
  • versions: for Illumina and Nanopore
  • pangoversion: for pangolin typing
• Illumina analysis additional features
  • flagstat
  • depth
  • VEP annotation
• Illumina results works for sc2reporter visualization
• Nanopore analysis additional features (artic & medaka)
  • fastqc
  • multiqc
  • pycoQC (only for artic)

v1.8.0

Minor updates

• Pangolin v4 support
• Updated Picard arguments
• FastQC commands can be added from config
• Added version of pangolin to build_dockerfile

Bug fixes

• Fixed build_dockerfile
• Fixed R issue
• Fixed mamba issue

Major changes

• The illumina and nanopore tracks automatically run pangolin and nextclade.
• Generates report for base changes.

Pipeline Diagram

Find DAG and other figures here

Requirements

• Nextflow version >=20.10, <22.0 (tested OK on NextFlow version 20.10.0, version 21.10.6)
• Singularity version 3.7.1 (tested OK)
• Conda version >= 4.13.0 (tested OK)

Quick Start Guide

Test Data

To test the pipeline, an example dataset for both Illumina and Nanopore (nanopolish, medaka) datafiles (from ConnerLab) provided.

parameters setup

primer scheme

--scheme: To use the primer list, add --scheme to the CLI, eg., use 'nCoV-2019/V3' for artic primers or 'midnight-primer/V1'

--scheme nCoV-2019/V3/
--scheme midnight-primers/V1/
--scheme eden-primers/V1/

To run the artic pipeline, please change the nanopore.config 'min_length' (default = 400) and 'max_length' (default = 700)

For more parameters setup, please see the ConnerLab documentation

Run on local server

Requirements

1. Containers: Singularity, Docker
2. Nextflow>=20

Illumina pipeline

nextflow run main.nf -profile singularity \
    --illumina --prefix "test_illumina"     \
    --directory .github/data/fastqs/    \
    --outdir illumina_test

Nanopore nanopolish pipeline

nextflow run main.nf -profile singularity \
    --nanopolish --prefix "test_nanopore_nanopolish" \
    --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
    --fast5_pass .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fast5_pass/ \
    --sequencing_summary .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/sequencing_summary_FAK72834_298b7829.txt \
    --outdir nanopore_nanopolish

Nanopore medaka pipeline

nextflow run main.nf -profile singularity \
    --medaka --prefix "test_nanopore_medaka" \
    --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
    --outdir nanopore_medaka

Run on NGP server

Datafile structure

1. for Nanopore analysis (default is "midnight")

   sample_name
        |___ fast5_pass/
        |___ fastq_pass/
        |___ sequencing_summary.txt

   Run Nanopolish pipeline

   nextflow run main.nf -profile singularity,sge \
   --nanopolish --prefix "test_nanopore" \
   --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
   --fast5_pass .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fast5_pass/ \
   --sequencing_summary .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/sequencing_summary_FAK72834_298b7829.txt \
    --outdir nanopore_test

Run medaka pipeline

nextflow run main.nf -profile singularity,sge \
    --medaka --prefix "test_nanopore_medaka" \
    --basecalled_fastq .github/data/nanopore/20200311_1427_X1_FAK72834_a3787181/fastq_pass/ \
    --outdir nanopore_medaka

2. for Illumina analysis

   sample_name     
        |___ fastq/

   Run Illumina pipeline

   nextflow run main.nf -profile singularity,sge \
   --illumina --prefix "test_illumina"     \
   --directory .github/data/fastqs/    \
   --outdir illumina_test

Useful information

1.To update your container image to the latest version from dockerhub, please delete your local image first before running the analysis pipeline.