I was using the sci-demux and the newer versions of Nextflow default to using DSL2 (https://www.nextflow.io/docs/latest/dsl2.html) which has removed certain operators (like into). This resulted in a silent error in failing to make good_sample_sheet
A work around was to add the line nextflow.enable.dsl=1 to my config file.
Either rewriting the nextflow code to remove the deprecated operators or altering the README to suggest the change to the .config might be in order.
Thanks!