Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests

Open kornkv opened this issue 1 month ago • 2 comments

draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests

Dec 08 '25 10:12 kornkv

Note for reviewers: `setup-nextflow` deletion is intentional cleanup

The diff shows deletion of a setup-nextflow submodule entry - this is correct and beneficial, not an error.

setup-nextflow is the nf-core/setup-nextflow GitHub Action for installing Nextflow in CI
It was accidentally committed as an orphaned git submodule in PR #8895 (2025-08-18) - likely from a contributor's local dev environment
There's no corresponding .gitmodules file, making it a broken/orphaned gitlink
Previous removal attempts in PRs #8977 and #9095 were undone when PR #9333 merge reintroduced it

The removal commit by @vagkaratzas (9239334ea - "remove unused folder") correctly cleans this up.

Dec 16 '25 11:12 pinin4fjords

I wonder a bit how it fits into the landscape of other trimming/ preprocessing workflows, but nothing particularly objectionable

Thanks! I'll wait for @jfy133 for a final review pass and will then merge. Stay tuned for the following updates :D

Dec 16 '25 14:12 vagkaratzas