add testing#58
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Pull request overview
This PR updates the nf-test expectations and adds a Nextflow stub: implementation for the find_switchback_reads module so the workflow can run under -stub-run while still producing the expected switchbacks outputs.
Changes:
- Added a
stub:block tomodules/find_switchback_reads.nfthat creates placeholder.switchbacks.bamand.switchbacks.summary.txtoutputs. - Updated
tests/main.nf.test.snapto reflect the additional tasks and the new--fgbio_switchbacksargument appearing in the aggregated arguments output.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| tests/main.nf.test.snap | Updates snapshots for task counts and aggregated arguments to include the switchbacks summary input. |
| modules/find_switchback_reads.nf | Adds a stub: script to generate placeholder switchbacks outputs during -stub-run testing. |
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