implications of the strict syntax to main.nf and nextflow.config

strict syntax (https://www.nextflow.io/docs/latest/strict-syntax.html) makes it so we cannot:

• mix declarations and statements (https://www.nextflow.io/docs/latest/strict-syntax.html#mixing-script-declarations-and-statements)
• add anything other than statements to config files (https://www.nextflow.io/docs/latest/strict-syntax.html#configuration-syntax)

however, the current main.nf and nextflow.config do not follow this convention.