Config files

A FILE THAT THE END USER CAN COPY AND EDIT IS FOUND AT configs/cecret_config_template.config

Using config files

The End User should not have to change the files in the Cecret repository in order to get the analyses that they need. Nextflow has a wonderful system of config files, which are recommended. Please read nextflow's documentation about config files at https://www.nextflow.io/docs/latest/config.html

The general format of a config file is

param.<parameter that needs adjusting> = <what it needs to be adjusted to>

Then this config file is used with the workflow via the following

nextflow run UPHL-BioNGS/Cecret -c <path to custom config file>

In theory, the values specified in this config file will be used over the defaults set in the workflow.

Example usage

In this example case, an end user would like to use this workflow for some amplicon-based library prep of a new virus impacting human health. The end user would need to add in some reference files as well as adjust some of the parameters of the workflow. Their fastq files are already prepared in a sample sheet.

Here's a list of what they want to adjust:

• reference file
• gff file
• amplicon scheme bedfile
• primer scheme bedfile
• remove duplicates
• supply a kraken2 database
• use minimap2 instead of bwa for mapping/alignment
• use docker for container management

Hypothetical config file for this new virus:

docker.enabled = true
docker.runOptions = "-u \$(id -u):\$(id -g)"
params.primer_bed = '/Volumes/new_virus/primer_schemes/V9_primer.bed'
params.amplicon_bed = '/Volumes/new_virus/primer_schemes/V9_amplicon.bed'
params.reference_genome = '/Volumes/new_virus/reference.fasta'
params.gff = '/Volumes/new_virus/reference.gff'
params.kraken2 = true
params.kraken2_db = '/Volumes/Kraken2_db/'
params.markdup = true
params.relatedness = true
params.species = 'other'
params.pangolin = false
params.freyja = false
params.nextclade = false
params.vadr = false
params.aligner = 'minimap2'

Corresponding usage on the command line

nextflow run UPHL-BioNGS/Cecret -c new_virus.config --sample_sheet sample_sheet.csv