Define where the pipeline should find input data and save output data.
Options for the reference genome indices used to align reads.
Options exclusive to running the pipeline on Nanopore data using the ARTIC fieldbioinformatics pipeline.
Options common to both the Nanopore and Illumina workflows in the pipeline.
Options to adjust QC, read trimming and host read filtering with Kraken2 for the Illumina workflow.
Various options for the variant calling branch of the Illumina workflow.
Various options for the de novo assembly branch of the Illumina workflow.
Less common options for the pipeline, typically set in a config file.
Set the top limit for requested resources for any single job.
Parameters used to describe centralised config profiles. These should not be edited.