Pipeline configuration

When a nextflow pipeline is built with FlowCraft, a number of configuration files are automatically generated in the same directory. They are all imported at the end of the nextflow.config file and are sorted by their configuration role. All configuration files are overwritten if you build another pipeline in the same directory, with the exception of the user.config file, which is meant to be a persistent configuration file.


The params.config file includes all available paramenters for the pipeline and their respective default values. Most of these parameters already contain sensible defaults.


The resources.config file includes the majority of the directives provided for each process, including cpus and memory. You’ll note that each process name has a suffix like _1_1, which is a unique process identifier composed of <lane>_<process_number>. This ensures that even when the same component is specified multiple times in a pipeline, you’ll still be able to set directives for each one individually.


The containers.config file includes the container directive for each process in the pipeline. These containers are retrieved from dockerhub, if they do not exist locally yet. You can change the container string to any other value, but it should point to an image that exist on dockerhub or locally.


The profiles.config file includes a set of pre-made profiles with all possible combinations of executors and container engines. You can add new ones or modify existing one.

User configutations

The user.config file is configuration file that is not overwritten when a new pipeline is build in the same directory. It can contain any configuration that is supported by nextflow and will overwrite all other configuration files.