A Nextflow pipeline for providing public health bioinfo

Introduction

The bioinflow pipeline is a workflow that provides information on various pathogen genomics workflows utilized at the BCCDC-PHL. You can select specific pathogens of interest or collections of pathogens and it will return tools and tips curated for you.

Quick-start

nextflow run BCCDC-PHL/bioinflow \
  --input <input_file> \
  --name <your name>  \
  --all

Installation

An up-to-date version of Nextflow is required because the pipeline is written in DSL2. Follow the instructions at https://www.nextflow.io/ to download and install Nextflow.

Input

The input is a question file of format *.txt or *.md (either question.txt or question.md) in addition to the user's name. Which file format is used depends on the pathogen of interest. The workflows and corresponding input file format is specified below:

Option	Input Type	Workflow
--pathogen flu	*.txt	Influenza only.
--pathogen rsv	*.md	RSV only.
--pathogen tb	*.txt	TB only.
--pathogen sarscov2_ww	*.md	SARS-CoV-2 in wastewater only.
--pathogen sarscov2_clin	*.md	Clinical SARS-CoV-2 only.
--pathogen tpa	*.txt	Treponema pallidum subsp. pallidum only.
--all	*.txt or *.md	Retrieve information about all pathogen analyses
--resp	*.txt or *.md	Retrieve information about respiratory pathogen analyses
--virus	*.txt or *.md	Retrieve information about viral genomic analyses
--bact	*.txt or *.md	Retrieve information about bacterial genomic analyses

Config

Important config options are:

Option	Requirement	Description	Microbe
input	Mandatory	Absolute path to the input file.
name	Mandatory	Name of user. Used for logging and output directory.
all	Optional	Retrieve information about all pathogen analyses	flu, rsv, tb, sars-cov-2, treponema
resp	Optional	Retrieve information about respiratory pathogen analyses	flu, rsv, tb, sars-cov-2
virus	Optional	Retrieve information about viral genomic analyses	flu, rsv, sars-cov-2
bact	Optional	Retrieve information about bacterial genomic analyses	tb, treponema
pathogen	Optional	Retrieve information about single pathogen of interest	pathogen of interest
email	Optional	Enter your email to receive your results
question	Optional	Ask us a question. Ensure you use the --email param so we can get back to you
fun	Optional	Have a little fun

Output

A subdirectory for each process in the workflow is created in --outdir.