Migrate hello_nf-core to nf-core tools 4.0.2 + v2 parser#970
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pinin4fjords wants to merge 3 commits into
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Migrate hello_nf-core to nf-core tools 4.0.2 + v2 parser#970pinin4fjords wants to merge 3 commits into
pinin4fjords wants to merge 3 commits into
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…-schema 2.7.2, v2-clean All 5 solutions run to completion under Nextflow 26.04.4 v2 parser. validate_params handled via config boolean in parts 2-4 (preserves lesson 5's schema-validation exercise); part 5 keeps the greetings schema + validation on. [skip ci]
Runs under the 26.04 default v2 parser (no NXF_SYNTAX_PARSER=v1). Boolean params set via params-file/config instead of bare CLI flags (which the v2 parser types as strings). Orientation rewritten to v2 + nf-core 4.0.2; devcontainer pin -> 4.0.2. All console output regenerated from genuine 4.0.2/v2 runs on x86. [skip ci]
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Modernizes the hello_nf-core course from nf-core tools 3.5.2 → 4.0.2 so it runs under the Nextflow 26.04 default v2 parser, removing the
NXF_SYNTAX_PARSER=v1workaround that #969 keeps as an interim.Why this is a separate PR
#969 leaves hello_nf-core working under v1 (the honest interim: the course was built for the 3.5.2 template, which isn't v2-clean). Getting it onto the v2 default is a different axis - an nf-core tools/template upgrade - so it's stacked rather than folded in.
What changed
core-hello-start,part2-part5) verified running to completion under the v2 parser on native x86.validate_params: the--validate_params falseCLI flag is a no-op under v2 (bare CLI values are typed as strings;"false"is truthy - Using strict syntax causes template to raise an error when setting boolean options on CLI nf-core/tools#4100). Parts 2-4 now setvalidate_params = falsein config (a real boolean), preserving the Part 5 lesson that teaches the schema-validation transformation. The CLI flag is gone from all commands.nf-core/tools version 4.0.2create banner and theGenerated container configs...line.-params-file/config, not bare CLI flags (the v2 string-typing behavior - it also affected Part 1's--skip_trim, now shown via a params file).uv-toolspin →nf-core==4.0.2.Known 4.0 behavior documented
nf-core modules installraisesNotADirectoryErroron the course's single-file local modules (4.0 expects directory-style); the install still completes, so Part 3 now verifies viamodules.jsonwith a warning admonition.Not verified (inherent)
Interactive nf-core TUIs (
pipelines create,schema build,modules create) can't be driven headlessly; their banners/versions are genuine 4.0.2, the click-through steps are unchanged.🤖 Generated with Claude Code