Linting in nf-core tools appears to require that params are set in nextflow.config and nextflow_schema.json

[scwatts]

Description of the bug

• conflicts with assigning reference input files to top-level key
  • i.e params.fasta is defined in nextflow_schema.json but not nextflow.config and assigned in main.nf
• currently resolved/circumvented in oncoanalyser by
  • lifting up all reference data into params.ref_data since this is ignored by linting
  • removing relevant entries from both nextflow_schema.json and nextflow.config
• primary impact of this to users is the absence of reference files paths in the pipeline summary/splash

Command used and terminal output

No response

Relevant files

No response

System information

No response

[scwatts]

Resolved by #16