refactor: compose test_prokaryotic profile on prokaryotic#1734
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Make test_prokaryotic include prokaryotic.config first, then layer test-specific settings on top. This removes duplicated prokaryotic params from test_prokaryotic.config (prokaryotic flag, aligner, gffread, featurecounts_feature_type, skip_bigwig, skip_rseqc, skip_dupradar, skip_qualimap) since they are now inherited. The nf-test params blocks in tests/prokaryotic.nf.test are kept as-is since CI runs those tests with -profile test,docker (not test_prokaryotic), so the params block is the mechanism that sets prokaryotic behavior in CI. Addresses review feedback from @adamrtalbot in PR #1717. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Feb 27, 2026
| includeConfig 'conf/prokaryotic.config' | ||
| includeConfig 'conf/test_prokaryotic.config' | ||
| } | ||
| prokaryotic { includeConfig 'conf/prokaryotic.config' } |
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Poor prokaryotic profile feels out of place down here with all the test profiles 😆
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Feb 27, 2026
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Better!
One more question, can we set profiles within nf-tests? I don't think I've tried 🤔
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You can set it in global config (though I stopped doing that when I added GPU stuff), but I don't think you can in tests themselves |
This was referenced Feb 27, 2026
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Summary
Make
test_prokaryoticcompose on theprokaryoticprofile rather than duplicating all its settings.nextflow.config:test_prokaryoticnow includesprokaryotic.configfirst, then layerstest_prokaryotic.configon topconf/test_prokaryotic.config: Remove 16 lines of duplicated prokaryotic settings (prokaryotic flag, aligner, gffread, featurecounts_feature_type, skip_bigwig, skip_rseqc, skip_dupradar, skip_qualimap) since they are now inherited fromprokaryotic.configThe nf-test params blocks in
tests/prokaryotic.nf.testare kept as-is since CI runs those tests with-profile test,docker(not-profile test_prokaryotic), so the params block is the mechanism that configures prokaryotic behavior in CI.Addresses review feedback from @adamrtalbot in PR #1717 regarding test/profile/param scoping.
Test plan
nextflow run . -profile test_prokaryotic,docker --outdir resultsproduces the same output as before🤖 Generated with Claude Code