Code

Stand alone schema#584

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drpatelh merged 27 commits intonf-core:devnf-core/tools:devfrom ewels:stand-alone-schemaewels/nf-core-tools:stand-alone-schemaCopy head branch name to clipboardMar 17, 2020

+891-14

Commits

Commits on Mar 17, 2020

• First draft of a parameters.settings.json file for the template

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• Fix JSON for template JSONschema file

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• Start writing new nf-core schema commands.

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• Start building 'nf-core schema build' functionality

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• Testing and refining code for building JSON Schema

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• Wrote code to handle interaction with nf-core website schema builder

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• Encode JSON schema in POST request

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• Final testing and tweaks for schema builder command

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• Rename parameters.settings.json > nextflow_schema.json

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• Schema: Rename Input to params

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• Add option --web_only for nf-core schema build

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• Hyphens for cli flags, not underscores

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• Update pipeline template schema

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• Schema: Handle groups when checking for missing or incorrect params

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• Template schema: Add some help text.

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• Remove top-level params object

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• Added nf-core schema validate functionality

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• Raise exceptions instead of sys.exit(1)

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• Add schema linting to main lint call

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• Added new params from the template update

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• Schema: If no existing schema found, create a new one from scratch

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• Added schema lint test to look for missing or unexpected params in schema

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• Reordered nf-core schema subcommands in help

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• Wrote documentation for nf-core schema

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• Rename schema use_defaults to no_prompts

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• Fix lint pytests

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• Remove dup blank line in readme

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