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.
Removal of adapters, paired-end merging, poly-G removal etc.
Options for aligning reads against reference genome(s)
Options related to length, quality, and map status filtering of reads.
Options to related to metagenomic screening.
Options for removal of PCR duplicates
Options for filtering for, trimming or rescaling characteristic ancient DNA damage patterns
Options for variant calling
Options for the calculation of ratio of reads to one chromosome/FASTA entry against all others.
Options for calculating and filtering for characteristic ancient DNA damage patterns.
Options for getting reference annotation statistics (e.g. gene coverages)
Options for the estimation of contamination