Fix post-ar trimming not being included in downstream analyses

I accidently left debugging code rather than mixxing the trimmed files back into the input channel for lane merging 🤦‍♀

PR checklist

[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
- [x] If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
- [x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
- [x] If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint .).
[x] Ensure the test suite passes (nextflow run . -profile test,docker).
[x] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).

To cloe #822