A pipeline to check for certain taxa in fastq files and optionally filter out this taxonomic group
Parameters which control the workflow.
Parameters used by kraken2 to classify all reads provided. Fine-tuning of the isolation step can be done via the cutoff_* parameters. The taxon for assessing/filtering can be set using tax2filter.
Parameters to fine-tune the output of blastn.
Quality control of raw reads.
Options to control the behavior of fastp
Define where the pipeline should find input data and save output data.
Reference genome related files and options required for the workflow.
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.