Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Define where the pipeline should find input data and save output data.
Common options across both long and short read preprocessing QC steps
Options for adapter clipping, quality trimming, pair-merging, and complexity filtering
Options for adapter clipping, quality trimming, and length filtering
Options for pre-profiling host read removal
Options for per-sample run-merging
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.
Reference genome related files and options required for the workflow.