Fix lint: preserve underscores for subworkflow includes via full path#4074
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pinin4fjords merged 7 commits intodevfrom Mar 3, 2026
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…es via full path When a subworkflow includes another subworkflow using the full path (e.g., `../../../subworkflows/nf-core/vcf_gather_bcftools`), the linter incorrectly converted underscores to slashes, producing `vcf/gather/bcftools` instead of `vcf_gather_bcftools`. This happened because the `../../../` prefix check assumed all full-path includes were modules (where underscore-to-slash conversion is correct). Subworkflow includes via full paths also start with `../../../` but should preserve underscores since subworkflow directory names use them. The fix checks whether the include path contains `subworkflows/` before deciding how to derive the component name. Fixes #4073 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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mashehu
requested changes
Mar 2, 2026
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
mashehu
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Mar 3, 2026
Cover full-path subworkflow includes (underscore preservation), full-path module includes (underscore-to-slash conversion), relative subworkflow includes, and mixed include scenarios. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…b.com:nf-core/tools into fix/subworkflow-include-underscore-conversion
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
mashehu
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looking great now. Thanks!
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Summary
get_components_to_install()to check whether a full-path include (../../../...) points to a subworkflow or module before deriving the component namesubworkflows/in the path) now preserve underscores and are correctly added to the subworkflows dictProblem
When a subworkflow includes another subworkflow using the full path:
include { VCF_GATHER_BCFTOOLS } from '../../../subworkflows/nf-core/vcf_gather_bcftools'The linter converted the name to
vcf/gather/bcftools(splitting on underscores), causing ameta_includelint failure even whenmeta.ymlcorrectly listsvcf_gather_bcftoolsin components.This is because the
../../../path prefix check assumed all full-path includes were modules. Relative subworkflow includes (../vcf_gather_bcftools) worked fine since they hit a different code path.Context
Encountered in nf-core/modules#10283
Fixes #4073
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