nextflow is interpreting some command line option values as booleans when should be strings

[stenglein-lab]

This may relate to how nextflow parses/interprets the values of command line options. Nextflow is interpreting this as a boolean and converting the parameter value to (boolean) true

Passed to the nextflow command line:

// with this usage, params.bowtie2_options will have a value of true
 --bowtie2_options '--end-to-end'

Introducing an extra space before the -- causes nextflow to interpret it (properly) as a string

Passed to the nextflow command line:

 --bowtie2_options ' --end-to-end'

Or adding in additional text to the string causes nextflow to keep it as a string

Passed to the nextflow command line:

 --bowtie2_options '--end-to-end --sensitive'

Using parameter schema would probably fix this. Ditto upgrading to nextflow 26.04 (this is happening in 25.10.4). This seems related.