A glob matched nothing, so the process never ran at all
When a file pattern matches nothing the channel is empty and any process consuming it is simply skipped — often with no loud error. The usual culprit is quoting: an unquoted glob is expanded by your shell before the workflow ever sees it, so the workflow receives one filename instead of the pattern.
Always quote glob patterns on the command line: --reads '*_{1,2}.fastq.gz'. Then test the pattern with ls using the exact same quoting to confirm it matches what you expect, including the paired-end braces.