restructure config files
Closed this issue · 1 comments
hkaspersen commented
The pipeline should be able to run without needing to manually change values in a config file, as mentioned in the JOSS review (openjournals/joss-reviews#4677). The config files should hold the recommended, default values for different analyses, while the user should only have to change parameters that deviate from the default when running the pipeline run command. See nf-core pipelines for good examples.
hkaspersen commented
Old, manual config file removed. Added a new example config file in conf/base.config that users may use as a template for their systems, as mentioned in #27 (comment), openjournals/joss-reviews#4677 (comment), and openjournals/joss-reviews#4677 (comment).