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feat: convert to parameter types - #316

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maxulysse wants to merge 6 commits into
nf-core:devfrom
maxulysse:feature/parameter-types
Draft

feat: convert to parameter types#316
maxulysse wants to merge 6 commits into
nf-core:devfrom
maxulysse:feature/parameter-types

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@maxulysse

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Description

Convert pipeline to use parameter types as described in the nf-core blog post.

Changes

  • Add typed params block in main.nf
  • Migrate igenomes.config to Map structure (nested params deprecated)
  • Import standard nf-core utils subworkflows (utils_nextflow_pipeline, utils_nfschema_plugin, utils_nfcore_pipeline)
  • Update local utils subworkflow to use nf-core utils
  • Resolve genome params from genomes map
  • Bump nf-schema to 2.7.2
  • Bump Nextflow version requirement to 26.04.0

TODO

  • Fix StackOverflowError with Path types
  • Test pipeline execution
  • Update documentation

maxulysse added 6 commits July 1, 2026 13:46
- Add typed params block in main.nf
- Migrate igenomes.config to Map structure
- Import standard nf-core utils subworkflows
- Update local utils subworkflow to use nf-core utils
- Resolve genome params from genomes map
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