gpha-mscape-nf-strep-pneumo

This repository contains a nextflow pipeline and associated scripts for the characterisation of Streptococcus pneumoniae in metagenomic samples.

Installation

To clone this repo:
git clone git@github.com:ukhsa-collaboration/gpha-mscape-nf-strep-pneumo.git

No further installation is required for use on Bryn as the nextflow pipeline is containerised and will pull in relevant containers as required when the pipeline is run.

Usage

Example command:

nextflow run main.nf \
--samplesheet /path/to/samplesheet.csv \
--taxid 1313 \
--extract_reads True \
--outdir /path/to/outdir \
--server server-name \
--bucket "name-of-s3-bucket"

Parameters

Parameter	Description
samplesheet	Path to csv file containing sample information. Requires following columns: climb_id, fastq_1, fastq_2, kraken_output, kraken_report.
taxid	NCBI taxon ID to extract reads for
extract_reads	Boolean specifying if taxon reads should be extracted from fastq before running pneumokity
outdir	Path to output directory
server	Name of server working on
bucket	Name of s3 bucket to upload result files to

Pipeline overview

The pipeline consists of the following steps:

1. (Optional) Extracts reads for taxon of interest from a sample e.g. all reads classified as Streptoccocus or below (taxid: 1301), or all reads classified as Streptococcus pneumoniae (taxid: 1313).
2. Run pneumokity on reads (extracted by taxon or all reads in the sample). Pneumokity is a kmer-based serotyping tool from Streptoccocus pneumoniae.
3. Collate pneumokity results into the format required for onyx. This includes adding the vaccine status of the identified serotype if pneumokity ran successfully.
4. Creation of an onyx analysis table and adding any results files produced by pneumokity to s3 storage.
5. Publishing of the onyx analysis table.

Current pipeline structure

Long read typing workflow:

longread_typing
|-- longread_kmer_serotyping
    |-- run_kractor (optional)
    |-- run_pneumokity

|-- collate_serotyping_results
    |-- create_pneumokity_onyx_json
    |-- onyx_write
    |-- s3_upload (pneumokity success only)
    |-- onyx_update (pneumokity success only)
    |-- onyx_publish

Future additions

The following elements may be added in future versions of the pipeline:

• Streptococcus pneumoniae speciation - integration of the code used to confirm if samples containing Streptococcus reads contain Streptococcus pneumoniae as a workflow to run before longread_typing.
• PneumoCAT2 typing - addition of an extra mapping-based typing method in longread_typing for extra verification and added resolution for difficult to resolve serotypes.