Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
Define where the pipeline should find input data and save output data.
Reference genome related files and options required for the workflow.
Options to skip various steps within the workflow.
Options to adjust read trimming criteria.
Options to adjust inital circular DNA identifier
Parameters used to run Circle-Map.
Parameters used to run Circle_finder.
Parameters used to run Unicycler.
parameters used to run ampliconarchitect. The software needs additional data files not included in
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.