diff --git a/.github/workflows/deploy-preview..yml b/.github/workflows/deploy-preview..yml new file mode 100644 index 0000000..0a92a4f --- /dev/null +++ b/.github/workflows/deploy-preview..yml @@ -0,0 +1,29 @@ +name: Deploy PR previews + +on: + pull_request: + types: + - opened + - reopened + - synchronize + - closed + +concurrency: preview-${{ github.ref }} + +jobs: + deploy-preview: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - uses: actions/setup-python@v6 + with: + python-version: 3.x + - uses: astral-sh/setup-uv@v7 + - run: uv run generate_schema_docs.py --all + - run: uv run zensical build --clean + + - name: Deploy preview + uses: rossjrw/pr-preview-action@v1 + with: + source-dir: ./site/ + preview-branch: gh-pages diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..21edaca --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,31 @@ +name: build documentation +on: + push: + branches: + - main +permissions: + contents: read + pages: write + id-token: write +concurrency: + group: pages + cancel-in-progress: false +jobs: + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - uses: actions/configure-pages@v5 + - uses: actions/setup-python@v6 + with: + python-version: 3.x + - uses: astral-sh/setup-uv@v7 + - run: uv run generate_schema_docs.py --all + - run: uv run zensical build --clean + + - uses: JamesIves/github-pages-deploy-action@v4 + with: + folder: site # The folder the action should deploy. diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 6b56e69..cdb8c82 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -7,6 +7,6 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - - uses: pre-commit/action@v3.0.0 + - uses: actions/checkout@v6 + - uses: actions/setup-python@v6 + - uses: j178/prek-action@v1 diff --git a/.gitignore b/.gitignore index 5509140..6e2b7a3 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,3 @@ *.DS_Store +.cache +site diff --git a/README.md b/README.md index 14a18ef..4d92706 100644 --- a/README.md +++ b/README.md @@ -14,21 +14,30 @@ Each folder contains the schema (`schema.json`) and a `tests` folder with test c ### Prettier formatting We use [Prettier](https://prettier.io/) to format all files in this repository. -We use [pre-commit](https://pre-commit.com/) to run Prettier on all files before committing. +We use [prek](https://prek.j178.dev/) to run Prettier on all files before committing. To install the pre-commit hooks, run the following command: ```bash -pre-commit install +prek install ``` To run Prettier on all files, run the following command: ```bash -pre-commit run --all-files +prek run --all-files ``` -This is done automatically when committing. +### Building Documentation + +Serve documentation locally: + +```bash +uv sync --dev +uv run zensical serve +``` + +Then open `http://127.0.0.1:8000` in your browser. ### Testing schemas diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..2b6c4fc --- /dev/null +++ b/docs/index.md @@ -0,0 +1,15 @@ +--- +hide: + - toc +--- + +# Introduction + +Welcome to the Nextflow Schemas documentation. This repository contains JSON schemas used by Nextflow for validating pipeline inputs and plugin specifications. + +## Overview + +This repository provides two main schemas: + +- **[Pipeline Schema](schemas/pipeline/v1/schema)**: Validates Nextflow pipeline input specifications, including parameter definitions, validation rules, and parameter grouping +- **[Plugin Schema](schemas/plugin/v1/schema)**: Validates Nextflow plugin specifications, including configuration scopes and function definitions diff --git a/docs/schemas/pipeline/v1/schema.md b/docs/schemas/pipeline/v1/schema.md new file mode 100644 index 0000000..b10736b --- /dev/null +++ b/docs/schemas/pipeline/v1/schema.md @@ -0,0 +1,1004 @@ +# Nextflow pipeline input schema + +**Title:** Nextflow pipeline input schema + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +**Description:** Schema to validate Nextflow pipeline input specs + +| Property | Type | +| ----------------------------------------- | --------------- | +| + [$schema](#schema) | string | +| + [$id](#id) | string | +| + [title](#title) | string | +| + [description](#description) | string | +| + [type](#type) | const | +| - [$defs](#defs) | object | +| - [properties](#properties) | object | +| - [dependentRequired](#dependentRequired) | object | +| - [allOf](#allOf) | array of object | + +## `$schema` + +**Title:** schema + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +## `$id` + +**Title:** ID URI + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +## `title` + +**Title:** Title + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +## `description` + +**Title:** Description + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +## `type` + +**Title:** Top level type + +| | | +| ------------ | ------- | +| **Type** | `const` | +| **Required** | Yes | + +Specific value: `"object"` + +## `$defs` + +**Title:** Parameter groups + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +**Description:** A slightly strange use of a JSON schema standard that we use for Nextflow schema is `$defs`. + +JSON schema can group variables together in an `object`, but then the validation expects this structure to exist in the data that it is validating. +In reality, we have a very long "flat" list of parameters, all at the top level of `params.foo`. + +In order to give some structure to log outputs, documentation and so on, we group parameters into `$defs`. +Each `def` is an object with a title, description and so on. +However, as they are under `$defs` scope they are effectively ignored by the validation and so their nested nature is not a problem. +We then bring the contents of each definition object back to the "flat" top level for validation using a series of `allOf` statements at the end of the schema, +which reference the specific definition keys. + +| Property | Type | +| ------------------------- | ------ | +| - [^.\*$](#defs_pattern1) | object | + +### `^.*$` + +> All properties whose name matches the regular expression +> `^.*$` ([Test](https://regex101.com/?regex=%5E.%2A%24)) +> must respect the following conditions + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| ------------------------------------------------------- | ------ | +| + [title](#defs_pattern1_title) | string | +| + [type](#defs_pattern1_type) | const | +| - [fa_icon](#defs_pattern1_fa_icon) | string | +| - [description](#defs_pattern1_description) | string | +| - [required](#defs_pattern1_required) | array | +| + [properties](#defs_pattern1_properties) | object | +| - [dependentRequired](#defs_pattern1_dependentRequired) | object | + +#### `title` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +#### `type` + +| | | +| ------------ | ------- | +| **Type** | `const` | +| **Required** | Yes | + +Specific value: `"object"` + +#### `fa_icon` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +| Restrictions | | +| --------------------------------- | ----------------------------------------------- | +| **Must match regular expression** | `^fa` [Test](https://regex101.com/?regex=%5Efa) | + +#### `description` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +#### `required` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +**Description:** Any parameters that _must_ be specified should be set as `required` in the schema. + +!!! tip + + Make sure you do set `null` as a default value for the parameter, otherwise it will have a value even if not supplied by the pipeline user and the required property will have no effect. + +This is not done with a property key like other things described below, but rather by naming +the parameter in the `required` array in the definition object / top-level object. + +For more information, see the [JSON schema documentation](https://json-schema.org/understanding-json-schema/reference/object.html#required-properties). + +#### `properties` + +| | | +| ------------------------- | ------------------------ | +| **Type** | `object` | +| **Required** | Yes | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/parameterOptions | + +| Property | Type | +| --------------------------------------------- | ----------- | +| - [^.\*$](#defs_pattern1_properties_pattern1) | Combination | + +##### `^.*$` + +> All properties whose name matches the regular expression +> `^.*$` ([Test](https://regex101.com/?regex=%5E.%2A%24)) +> must respect the following conditions + +| | | +| ------------------------- | ---------------- | +| **Type** | `combining` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| All of(Requirement) | +| ------------------------------------------------------------------ | +| [standardKeywords](#defs_pattern1_properties_pattern1_pattern2_i0) | +| [customKeywords](#defs_pattern1_properties_pattern1_pattern2_i1) | + +###### `standardKeywords` + +| | | +| ------------------------- | ------------------------ | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/standardKeywords | + +**Description:** Allowed standard JSON Schema properties. + +| Property | Type | +| ------------------------------------------------------------------------------------- | ---------------------------------------- | +| - [type](#defs_pattern1_properties_pattern1_pattern2_i0_type) | Combination | +| - [format](#defs_pattern1_properties_pattern1_pattern2_i0_format) | enum (of string) | +| - [pattern](#defs_pattern1_properties_pattern1_pattern2_i0_pattern) | string | +| - [description](#defs_pattern1_properties_pattern1_pattern2_i0_description) | string | +| - [default](#defs_pattern1_properties_pattern1_pattern2_i0_default) | integer, boolean, string, number or null | +| - [examples](#defs_pattern1_properties_pattern1_pattern2_i0_examples) | array | +| - [deprecated](#defs_pattern1_properties_pattern1_pattern2_i0_deprecated) | boolean | +| - [minLength](#defs_pattern1_properties_pattern1_pattern2_i0_minLength) | integer | +| - [maxLength](#defs_pattern1_properties_pattern1_pattern2_i0_maxLength) | integer | +| - [minimum](#defs_pattern1_properties_pattern1_pattern2_i0_minimum) | number | +| - [exclusiveMinimum](#defs_pattern1_properties_pattern1_pattern2_i0_exclusiveMinimum) | number | +| - [maximum](#defs_pattern1_properties_pattern1_pattern2_i0_maximum) | number | +| - [exclusiveMaximum](#defs_pattern1_properties_pattern1_pattern2_i0_exclusiveMaximum) | number | +| - [multipleOf](#defs_pattern1_properties_pattern1_pattern2_i0_multipleOf) | number | +| - [enum](#defs_pattern1_properties_pattern1_pattern2_i0_enum) | array | +| - [const](#defs_pattern1_properties_pattern1_pattern2_i0_const) | integer, boolean, string, number or null | + +###### `type` + +| | | +| ------------------------- | ---------------- | +| **Type** | `combining` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +**Description:** Variable type, taken from the [JSON schema keyword vocabulary](https://json-schema.org/understanding-json-schema/reference/type.html): + +- `string` +- `number` (float) +- `integer` +- `boolean` (true / false) +- `object` (currently only supported for file validation) +- `array` (currently only supported for file validation) + +Validation checks that the supplied parameter matches the expected type, and will fail with an error if not. + +This JSON schema type is _not_ supported: + +- `null` + +| Any of(Option) | +| ------------------------------------------------------------------------------ | +| [typeAnnotation](#defs_pattern1_properties_pattern1_pattern2_i0_type_anyOf_i0) | +| [item 1](#defs_pattern1_properties_pattern1_pattern2_i0_type_anyOf_i1) | + +###### `typeAnnotation` + +| | | +| -------------- | ---------------------- | +| **Type** | `enum (of string)` | +| **Required** | No | +| **Defined in** | #/$defs/typeAnnotation | + +Must be one of: + +- "string" +- "boolean" +- "integer" +- "number" +- "null" + +###### `item 1` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +| Each item of this array must be | Description | +| ------------------------------------------------------------------------------------ | ----------- | +| [typeAnnotation](#defs_pattern1_properties_pattern1_pattern2_i0_type_anyOf_i1_items) | - | + +###### typeAnnotation + +| | | +| ---------------------- | --------------------------------------------------------------------------------------------------------------------------- | +| **Type** | `enum (of string)` | +| **Required** | No | +| **Same definition as** | [defs_pattern1_properties_pattern1_pattern2_i0_type_anyOf_i0](#defs_pattern1_properties_pattern1_pattern2_i0_type_anyOf_i0) | + +###### `format` + +| | | +| ------------ | ------------------ | +| **Type** | `enum (of string)` | +| **Required** | No | + +**Description:** Formats can be used to give additional validation checks against `string` values for certain properties. + +!!! example "Non-standard key (values)" + + The `format` key is a [standard JSON schema key](https://json-schema.org/understanding-json-schema/reference/string.html#format), + however we primarily use it for validating file / directory path operations with non-standard schema values. + +Example usage is as follows: + +```json +{ + "type": "string", + "format": "file-path" +} +``` + +The available `format` types are below: + +`file-path` +: States that the provided value is a file. Does not check its existence, but it does check if the path is not a directory. + +`directory-path` +: States that the provided value is a directory. Does not check its existence, but if it exists, it does check that the path is not a file. + +`path` +: States that the provided value is a path (file or directory). Does not check its existence. + +`file-path-pattern` +: States that the provided value is a glob pattern that will be used to fetch files. Checks that the pattern is valid and that at least one file is found. + +Must be one of: + +- "file-path" +- "directory-path" +- "path" +- "file-path-pattern" +- "date-time" +- "date" +- "time" +- "email" +- "uri" +- "regex" + +###### `pattern` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | +| **Format** | `regex` | + +**Description:** Regular expression which the string must match in order to pass validation. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#regular-expressions) + for details. +- Use for help with writing regular expressions. + +For example, this pattern only validates if the supplied string ends in `.fastq`, `.fq`, `.fastq.gz` or `.fq.gz`: + +```json +{ + "type": "string", + "pattern": ".*.f(ast)?q(.gz)?$" +} +``` + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +###### `description` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** A short description of what the parameter does, written in markdown. +Printed in docs and terminal help text. +Should be maximum one short sentence. + +###### `default` + +| | | +| -------------- | ------------------------------------------ | +| **Type** | `integer, boolean, string, number or null` | +| **Required** | No | +| **Defined in** | #/$defs/allTypes | + +**Description:** Default value for the parameter. + +Should match the `type` and validation patterns set for the parameter in other fields. + +!!! tip + + If no default should be set, completely omit this key from the schema. + Do not set it as an empty string, or `null`. + + However, parameters with no defaults _should_ be set to `null` within your Nextflow config file. + +!!! note + + When creating a schema using `nf-core schema build`, this field will be automatically created based + on the default value defined in the pipeline config files. + + Generally speaking, the two should always be kept in sync to avoid unexpected problems and usage errors. + In some rare cases, this may not be possible (for example, a dynamic groovy expression cannot be encoded in JSON), + in which case try to specify as "sensible" a default within the schema as possible. + +###### `examples` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +**Description:** A list of examples for the current parameter + +| Each item of this array must be | Description | +| ------------------------------------------------------------------------- | ----------- | +| [allTypes](#defs_pattern1_properties_pattern1_pattern2_i0_examples_items) | - | + +###### allTypes + +| | | +| ---------------------- | ----------------------------------------------------------------- | +| **Type** | `integer, boolean, string, number or null` | +| **Required** | No | +| **Same definition as** | [default](#defs_pattern1_properties_pattern1_pattern2_i0_default) | + +###### `deprecated` + +| | | +| ------------ | --------- | +| **Type** | `boolean` | +| **Required** | No | + +**Description:** !!! example "Extended key" + +A boolean JSON flag that instructs anything using the schema that this parameter/field is deprecated and should not be used. This can be useful to generate messages telling the user that a parameter has changed between versions. + +JSON schema states that this is an informative key only, but in [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) this will cause a validation error if the parameter/field is used. + +!!! tip + + Using the [`errorMessage`](#errormessage) keyword can be useful to provide more information about the deprecation and what to use instead. + +###### `minLength` + +| | | +| -------------- | -------------------------- | +| **Type** | `integer` | +| **Required** | No | +| **Defined in** | #/$defs/nonNegativeInteger | + +**Description:** Specify a minimum / maximum string length with `minLength` and `maxLength`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#length) + for details. + +```json +{ + "type": "string", + "minLength": 2, + "maxLength": 3 +} +``` + +| Restrictions | | +| ------------ | ------ | +| **Minimum** | ≥ 0 | + +###### `maxLength` + +| | | +| ---------------------- | --------------------------------------------------------------------- | +| **Type** | `integer` | +| **Required** | No | +| **Same definition as** | [minLength](#defs_pattern1_properties_pattern1_pattern2_i0_minLength) | + +**Description:** Specify a minimum / maximum string length with `minLength` and `maxLength`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#length) + for details. + +```json +{ + "type": "string", + "minLength": 2, + "maxLength": 3 +} +``` + +###### `minimum` + +| | | +| ------------ | -------- | +| **Type** | `number` | +| **Required** | No | + +**Description:** Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range) + for details. + +> If x is the value being validated, the following must hold true: +> +> - `x` ≥ `minimum` +> - `x` ≤ `maximum` + +```json +{ + "type": "number", + "minimum": 0, + "maximum": 100 +} +``` + +!!! note + + The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys. + Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys. + However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them. + +###### `exclusiveMinimum` + +| | | +| ------------ | -------- | +| **Type** | `number` | +| **Required** | No | + +**Description:** Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range) + for details. + +> If x is the value being validated, the following must hold true: +> +> - `x` ≥ `minimum` +> - `x` ≤ `maximum` + +```json +{ + "type": "number", + "minimum": 0, + "maximum": 100 +} +``` + +!!! note + + The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys. + Because [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) uses stock JSON schema validation libraries, these _should_ work for validating keys. + However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them. + +###### `maximum` + +| | | +| ------------ | -------- | +| **Type** | `number` | +| **Required** | No | + +**Description:** Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range) + for details. + +> If x is the value being validated, the following must hold true: +> +> - `x` ≥ `minimum` +> - `x` ≤ `maximum` + +```json +{ + "type": "number", + "minimum": 0, + "maximum": 100 +} +``` + +!!! note + + The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys. + Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys. + However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them. + +###### `exclusiveMaximum` + +| | | +| ------------ | -------- | +| **Type** | `number` | +| **Required** | No | + +**Description:** Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range) + for details. + +> If x is the value being validated, the following must hold true: +> +> - `x` ≥ `minimum` +> - `x` ≤ `maximum` + +```json +{ + "type": "number", + "minimum": 0, + "maximum": 100 +} +``` + +!!! note + + The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys. + Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys. + However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them. + +###### `multipleOf` + +| | | +| ------------ | -------- | +| **Type** | `number` | +| **Required** | No | + +**Description:** The 'integer' or 'number' parameter value should be a multiple of this value + +###### `enum` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +**Description:** An array of enumerated values: the parameter must match one of these values exactly to pass validation. + +- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/generic.html#enumerated-values) + for details. +- Available for strings, numbers and integers. + +```json +{ + "enum": ["red", "amber", "green"] +} +``` + +| Each item of this array must be | Description | +| --------------------------------------------------------------------- | ----------- | +| [allTypes](#defs_pattern1_properties_pattern1_pattern2_i0_enum_items) | - | + +###### allTypes + +| | | +| ---------------------- | ----------------------------------------------------------------- | +| **Type** | `integer, boolean, string, number or null` | +| **Required** | No | +| **Same definition as** | [default](#defs_pattern1_properties_pattern1_pattern2_i0_default) | + +###### `const` + +| | | +| ---------------------- | ----------------------------------------------------------------- | +| **Type** | `integer, boolean, string, number or null` | +| **Required** | No | +| **Same definition as** | [default](#defs_pattern1_properties_pattern1_pattern2_i0_default) | + +**Description:** The parameter value should be equal to this value + +###### `customKeywords` + +| | | +| ------------------------- | ---------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/customKeywords | + +**Description:** Additional custom JSON Schema properties. + +| Property | Type | +| ----------------------------------------------------------------------------- | ------- | +| - [errorMessage](#defs_pattern1_properties_pattern1_pattern2_i1_errorMessage) | string | +| - [exists](#defs_pattern1_properties_pattern1_pattern2_i1_exists) | boolean | +| - [schema](#defs_pattern1_properties_pattern1_pattern2_i1_schema) | string | +| - [help_text](#defs_pattern1_properties_pattern1_pattern2_i1_help_text) | string | +| - [fa_icon](#defs_pattern1_properties_pattern1_pattern2_i1_fa_icon) | string | +| - [hidden](#defs_pattern1_properties_pattern1_pattern2_i1_hidden) | boolean | +| - [mimetype](#defs_pattern1_properties_pattern1_pattern2_i1_mimetype) | string | + +###### `errorMessage` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** +!!! example "Non-standard key" + +If validation fails, an error message is printed to the terminal, so that the end user knows what to fix. +However, these messages are not always very clear - especially to newcomers. + +To improve this experience, pipeline developers can set a custom `errorMessage` for a given parameter in a the schema. +If validation fails, this `errorMessage` is printed after the original error message to guide the pipeline users to an easier solution. + +For example, instead of printing: + +``` +* --input (samples.yml): "samples.yml" does not match regular expression [^\S+\.csv$] +``` + +We can set + +```json +"input": { + "type": "string", + "pattern": "^\S+\.csv$", + "errorMessage": "File name must end in '.csv' cannot contain spaces" +} +``` + +and get: + +``` +* --input (samples.yml): "samples.yml" does not match regular expression [^\S+\.csv$] (File name must end in '.csv' cannot contain spaces) +``` + +| Restrictions | | +| -------------- | --- | +| **Min length** | 1 | + +###### `exists` + +| | | +| ------------ | --------- | +| **Type** | `boolean` | +| **Required** | No | + +**Description:** When a format is specified for a value, you can provide the key `exists` set to true in order to validate that the provided path exists. Set this to `false` to validate that the path does not exist. + +Example usage is as follows: + +```json +{ + "type": "string", + "format": "file-path", + "exists": true +} +``` + +!!! note + + If the parameter is an S3, Azure or Google Cloud URI path, this validation is ignored. + +!!! warning + + Make sure to only use the `exists` keyword in combination with any file path format. Using `exists` on a normal string will assume that it's a file and will probably fail unexpectedly. + +###### `schema` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** Path to a JSON schema file used to validate _the supplied file_. + +Should only be set when `format` is `file-path`. + +!!! tip + + Setting this field is key to working with sample sheet validation and channel generation, as described in the sample sheet section of the [nf-schema docs](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/sample_sheet_schema_specification/). + +These schema files are typically stored in the pipeline `assets` directory, but can be anywhere. + +```json +{ + "type": "string", + "format": "file-path", + "schema": "assets/foo_schema.json" +} +``` + +!!! note + + If the parameter is set to `null`, `false` or an empty string, this validation is ignored. The file won't be validated. + +| Restrictions | | +| --------------------------------- | --------------------------------------------------------- | +| **Min length** | 1 | +| **Must match regular expression** | `\.json$` [Test](https://regex101.com/?regex=%5C.json%24) | + +###### `help_text` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** +!!! example "Non-standard key" + +A longer text with usage help for the parameter, written in markdown. +Can include newlines with multiple paragraphs and more complex markdown structures. + +Typically hidden by default in documentation and interfaces, unless explicitly clicked / requested. + +###### `fa_icon` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** +!!! example "Non-standard key" + +A text identifier corresponding to an icon from [Font Awesome](https://fontawesome.com/). +Used for easier visual navigation of documentation and pipeline interfaces. + +Should be the font-awesome class names, for example: + +```json +"fa_icon": "fas fa-file-csv" +``` + +| Restrictions | | +| --------------------------------- | ----------------------------------------------- | +| **Must match regular expression** | `^fa` [Test](https://regex101.com/?regex=%5Efa) | + +###### `hidden` + +| | | +| ------------ | --------- | +| **Type** | `boolean` | +| **Required** | No | + +**Description:** +!!! example "Non-standard key" + +A boolean JSON flag that instructs anything using the schema that this is an unimportant parameter. + +Typically used to keep the pipeline docs / UIs uncluttered with common parameters which are not used by the majority of users. +For example, `--plaintext_email` and `--monochrome_logs`. + +```json +"hidden": true +``` + +###### `mimetype` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +**Description:** MIME type for a file path. Setting this value informs downstream tools about what _kind_ of file is expected. + +Should only be set when `format` is `file-path`. + +- See a [list of common MIME types](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types) + +```json +{ + "type": "string", + "format": "file-path", + "mimetype": "text/csv" +} +``` + +###### The following properties are required + +- type +- description + +#### `dependentRequired` + +| | | +| ------------------------- | ------------------------------------------------------------------------------------------------------------ | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | [Each additional property must conform to the schema](#defs_pattern1_dependentRequired_additionalProperties) | + +| Property | Type | +| ----------------------------------------------------------- | --------------- | +| - [](#defs_pattern1_dependentRequired_additionalProperties) | array of string | + +##### `additionalProperties` + +| | | +| ------------ | ----------------- | +| **Type** | `array of string` | +| **Required** | No | +| **Default** | `[]` | + +| Each item of this array must be | Description | +| ----------------------------------------------------------------------------------------- | ----------- | +| [additionalProperties items](#defs_pattern1_dependentRequired_additionalProperties_items) | - | + +###### additionalProperties items + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +## `properties` + +| | | +| ------------------------- | --------------------------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Same definition as** | [properties](#defs_pattern1_properties) | + +## `dependentRequired` + +| | | +| ------------------------- | ---------------------------------------------------------------------------------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | [Each additional property must conform to the schema](#dependentRequired_additionalProperties) | + +| Property | Type | +| --------------------------------------------- | --------------- | +| - [](#dependentRequired_additionalProperties) | array of string | + +### `additionalProperties` + +| | | +| ------------ | ----------------- | +| **Type** | `array of string` | +| **Required** | No | +| **Default** | `[]` | + +| Each item of this array must be | Description | +| --------------------------------------------------------------------------- | ----------- | +| [additionalProperties items](#dependentRequired_additionalProperties_items) | - | + +#### additionalProperties items + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +## `allOf` + +**Title:** Combine definition groups + +| | | +| ------------ | ----------------- | +| **Type** | `array of object` | +| **Required** | No | + +| Each item of this array must be | Description | +| ------------------------------- | ----------- | +| [allOf items](#allOf_items) | - | + +### allOf items + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| -------------------------- | ------ | +| + [$ref](#allOf_items_ref) | string | + +#### `$ref` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | Yes | + +| Restrictions | | +| --------------------------------- | ----------------------------------------------------------------------------------------------- | +| **Must match regular expression** | `^#/\$defs/[^/]+$` [Test](https://regex101.com/?regex=%5E%23%2F%5C%24defs%2F%5B%5E%2F%5D%2B%24) | + +--- + +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) diff --git a/docs/schemas/plugin/v1/schema.md b/docs/schemas/plugin/v1/schema.md new file mode 100644 index 0000000..754ba8b --- /dev/null +++ b/docs/schemas/plugin/v1/schema.md @@ -0,0 +1,290 @@ +# Nextflow plugin schema + +**Title:** Nextflow plugin schema + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +**Description:** Schema for Nextflow plugin specs + +| Property | Type | +| ----------------------------- | ----- | +| - [definitions](#definitions) | array | + +## `definitions` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +| Each item of this array must be | Description | +| --------------------------------------- | ----------- | +| [definitions items](#definitions_items) | - | + +### definitions items + +| | | +| ------------------------- | ---------------- | +| **Type** | `combining` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Any of(Option) | +| ------------------------------------------- | +| [config_scope](#definitions_items_anyOf_i0) | +| [function](#definitions_items_anyOf_i1) | + +#### `config_scope` + +| | | +| ------------------------- | -------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/config_scope | + +| Property | Type | +| ------------------------------------------ | ---------------- | +| - [type](#definitions_items_anyOf_i0_type) | enum (of string) | +| - [spec](#definitions_items_anyOf_i0_spec) | object | + +##### `type` + +| | | +| ------------ | ------------------ | +| **Type** | `enum (of string)` | +| **Required** | No | + +Must be one of: + +- "ConfigScope" + +##### `spec` + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| ------------------------------------------------------------- | ------ | +| - [name](#definitions_items_anyOf_i0_spec_name) | string | +| - [description](#definitions_items_anyOf_i0_spec_description) | string | +| - [children](#definitions_items_anyOf_i0_spec_children) | array | + +###### `name` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `description` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `children` + +| | | +| ------------ | ------- | +| **Type** | `array` | +| **Required** | No | + +| Each item of this array must be | Description | +| ----------------------------------------------------------------- | ----------- | +| [children items](#definitions_items_anyOf_i0_spec_children_items) | - | + +###### children items + +| | | +| ------------------------- | ---------------- | +| **Type** | `combining` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Any of(Option) | +| ------------------------------------------------------------------------- | +| [config_scope](#definitions_items_anyOf_i0_spec_children_items_anyOf_i0) | +| [config_option](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1) | + +###### `config_scope` + +| | | +| ------------------------- | --------------------------------------------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Same definition as** | [definitions_items_anyOf_i0](#definitions_items_anyOf_i0) | + +###### `config_option` + +| | | +| ------------------------- | --------------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/config_option | + +| Property | Type | +| ----------------------------------------------------------------------- | ---------------- | +| - [type](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1_type) | enum (of string) | +| - [spec](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1_spec) | object | + +###### `type` + +| | | +| ------------ | ------------------ | +| **Type** | `enum (of string)` | +| **Required** | No | + +Must be one of: + +- "ConfigOption" + +###### `spec` + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| ------------------------------------------------------------------------------------------ | ------ | +| - [name](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1_spec_name) | string | +| - [description](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1_spec_description) | string | +| - [type](#definitions_items_anyOf_i0_spec_children_items_anyOf_i1_spec_type) | string | + +###### `name` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `description` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `type` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +#### `function` + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | +| **Defined in** | #/$defs/function | + +| Property | Type | +| ------------------------------------------ | ---------------- | +| - [type](#definitions_items_anyOf_i1_type) | enum (of string) | +| - [spec](#definitions_items_anyOf_i1_spec) | object | + +##### `type` + +| | | +| ------------ | ------------------ | +| **Type** | `enum (of string)` | +| **Required** | No | + +Must be one of: + +- "Factory" +- "Function" +- "Operator" + +##### `spec` + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| ------------------------------------------------------------- | --------------- | +| - [name](#definitions_items_anyOf_i1_spec_name) | string | +| - [description](#definitions_items_anyOf_i1_spec_description) | string | +| - [returnType](#definitions_items_anyOf_i1_spec_returnType) | string | +| - [parameters](#definitions_items_anyOf_i1_spec_parameters) | array of object | + +###### `name` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `description` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `returnType` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `parameters` + +| | | +| ------------ | ----------------- | +| **Type** | `array of object` | +| **Required** | No | + +| Each item of this array must be | Description | +| --------------------------------------------------------------------- | ----------- | +| [parameters items](#definitions_items_anyOf_i1_spec_parameters_items) | - | + +###### parameters items + +| | | +| ------------------------- | ---------------- | +| **Type** | `object` | +| **Required** | No | +| **Additional properties** | Any type allowed | + +| Property | Type | +| ---------------------------------------------------------------- | ------ | +| - [name](#definitions_items_anyOf_i1_spec_parameters_items_name) | string | +| - [type](#definitions_items_anyOf_i1_spec_parameters_items_type) | string | + +###### `name` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +###### `type` + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | + +--- + +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css new file mode 100644 index 0000000..cdcd68f --- /dev/null +++ b/docs/stylesheets/extra.css @@ -0,0 +1,17 @@ +.md-typeset h4 code { + font-size: 1.25rem; +} + +.md-typeset h5 code { + font-size: 1rem !important; +} +.md-typeset h6 { + font-size: 0.8rem !important; +} + +/* Hide empty table headers (headers with only whitespace) */ +.md-typeset table thead tr th:empty { + visibility: hidden; + padding: 0; + border: none; +} diff --git a/generate_schema_docs.py b/generate_schema_docs.py new file mode 100644 index 0000000..a4146fd --- /dev/null +++ b/generate_schema_docs.py @@ -0,0 +1,139 @@ +#!/usr/bin/env python3 +""" +Super simple schema documentation generator. +Uses json-schema-for-humans to generate markdown. +""" + +import re +import subprocess +from pathlib import Path +from typing import Optional + +from json_schema_for_humans.generate import generate_from_filename +from json_schema_for_humans.generation_configuration import GenerationConfiguration + + +def clean_headings(markdown: str) -> str: + """ + Remove "Property " and "Pattern Property " prefixes from markdown headings. + Converts: ###### Property `name` + To: ###### `name` + """ + # Remove "Property " prefix from headings + markdown = re.sub( + r'(#{2,})\s+Property\s+(.*)$', + r'\1 \3', + markdown, + flags=re.MULTILINE + ) + + # Remove "Pattern Property " prefix from headings + markdown = re.sub( + r'(#{2,})\s+Pattern Property\s+(.*)$', + r'\1 \3', + markdown, + flags=re.MULTILINE + ) + + + return markdown + + +def generate_docs(schema_path: Path, output_path: Optional[Path] = None) -> str: + """ + Generate documentation for a JSON schema file. + Uses json-schema-for-humans with standard md template. + """ + if not output_path: + output_path = schema_path.with_suffix('.md') + + # Use json-schema-for-humans to generate markdown + config = GenerationConfiguration( + template_name="md", + show_breadcrumbs=False, + show_toc=False, + collapse_long_descriptions=False, + link_to_reused_ref=True, + footer_show_time=False, + template_md_options={ + "show_array_restrictions": False, + "properties_table_columns": ['Property','Type'], + "show_heading_numbers": False, + }, + expand_buttons=True + ) + + # Ensure output directory exists before generating + output_path.parent.mkdir(parents=True, exist_ok=True) + + # Generate to temp location + temp_output = output_path.parent / f"temp_{output_path.name}" + generate_from_filename(schema_path, str(temp_output), config=config) + + # Read, clean up, and write final output + markdown = temp_output.read_text() + markdown = clean_headings(markdown) + output_path.write_text(markdown) + + # Clean up temp file + temp_output.unlink() + + print(f"Documentation generated: {output_path}") + return markdown + + +def main(): + """Main entry point.""" + import argparse + + parser = argparse.ArgumentParser( + description="Generate markdown documentation from JSON schemas" + ) + parser.add_argument("schema", nargs="?", type=Path, help="Path to JSON schema file") + parser.add_argument("-o", "--output", type=Path, help="Output markdown file") + parser.add_argument("--all", action="store_true", help="Generate docs for all schemas") + parser.add_argument("--output-dir", type=Path, help="Output directory (default: docs/schemas/)") + + args = parser.parse_args() + + generated_files = [] + + if args.all: + repo_root = Path(__file__).parent + schema_files = [ + f for f in repo_root.glob("**/schema.json") + if not any(p.startswith('.') for p in f.parts) + ] + + print(f"Found {len(schema_files)} schema files") + output_dir = args.output_dir or (repo_root / "docs" / "schemas") + + for schema_file in schema_files: + schema_dir = schema_file.parent.relative_to(repo_root) + if str(schema_dir) == ".": + output_file = output_dir / f"{schema_file.stem}.md" + else: + output_file = output_dir / schema_dir / f"{schema_file.stem}.md" + generate_docs(schema_file, output_file) + generated_files.append(output_file) + else: + if not args.schema: + parser.error("schema argument is required when not using --all") + output_file = args.output or args.schema.with_suffix(".md") + generate_docs(args.schema, output_file) + generated_files.append(output_file) + + # Run prek --files on all generated files + if generated_files: + print(f"\nRunning prek on {len(generated_files)} generated file(s)...") + try: + subprocess.run( + ["prek", "--files"] + [str(f) for f in generated_files], + capture_output=True + ) + except FileNotFoundError: + print("Warning: prek not found in PATH, skipping formatting") + + +if __name__ == "__main__": + main() diff --git a/pipeline/v1/schema.json b/pipeline/v1/schema.json index 49cd090..2325ecb 100644 --- a/pipeline/v1/schema.json +++ b/pipeline/v1/schema.json @@ -32,6 +32,7 @@ }, "$defs": { "title": "Parameter groups", + "description": "A slightly strange use of a JSON schema standard that we use for Nextflow schema is `$defs`.\n\nJSON schema can group variables together in an `object`, but then the validation expects this structure to exist in the data that it is validating.\nIn reality, we have a very long \"flat\" list of parameters, all at the top level of `params.foo`.\n\nIn order to give some structure to log outputs, documentation and so on, we group parameters into `$defs`.\nEach `def` is an object with a title, description and so on.\nHowever, as they are under `$defs` scope they are effectively ignored by the validation and so their nested nature is not a problem.\nWe then bring the contents of each definition object back to the \"flat\" top level for validation using a series of `allOf` statements at the end of the schema,\nwhich reference the specific definition keys.", "type": "object", "patternProperties": { "^.*$": { @@ -53,7 +54,8 @@ "type": "string" }, "required": { - "type": "array" + "type": "array", + "description": "Any parameters that _must_ be specified should be set as `required` in the schema.\n\n!!! tip\n\n Make sure you do set `null` as a default value for the parameter, otherwise it will have a value even if not supplied by the pipeline user and the required property will have no effect.\n\nThis is not done with a property key like other things described below, but rather by naming\nthe parameter in the `required` array in the definition object / top-level object.\n\nFor more information, see the [JSON schema documentation](https://json-schema.org/understanding-json-schema/reference/object.html#required-properties)." }, "properties": { "$ref": "#/$defs/parameterOptions" @@ -134,7 +136,7 @@ "description": "Allowed standard JSON Schema properties.", "properties": { "type": { - "description": "The type of the parameter value. Can be one or more of these: `['integer', 'boolean', 'number', 'string', 'null']`", + "description": "Variable type, taken from the [JSON schema keyword vocabulary](https://json-schema.org/understanding-json-schema/reference/type.html):\n\n- `string`\n- `number` (float)\n- `integer`\n- `boolean` (true / false)\n- `object` (currently only supported for file validation)\n- `array` (currently only supported for file validation)\n\nValidation checks that the supplied parameter matches the expected type, and will fail with an error if not.\n\nThis JSON schema type is _not_ supported:\n\n- `null`", "anyOf": [ { "$ref": "#/$defs/typeAnnotation" }, { @@ -145,7 +147,7 @@ }, "format": { "type": "string", - "description": "The format of a parameter value with the 'string' type. This is used for additional validation on the structure of the value.", + "description": "Formats can be used to give additional validation checks against `string` values for certain properties.\n\n!!! example \"Non-standard key (values)\"\n\n The `format` key is a [standard JSON schema key](https://json-schema.org/understanding-json-schema/reference/string.html#format),\n however we primarily use it for validating file / directory path operations with non-standard schema values.\n\nExample usage is as follows:\n\n```json\n{\n \"type\": \"string\",\n \"format\": \"file-path\"\n}\n```\n\nThe available `format` types are below:\n\n`file-path`\n: States that the provided value is a file. Does not check its existence, but it does check if the path is not a directory.\n\n`directory-path`\n: States that the provided value is a directory. Does not check its existence, but if it exists, it does check that the path is not a file.\n\n`path`\n: States that the provided value is a path (file or directory). Does not check its existence.\n\n`file-path-pattern`\n: States that the provided value is a glob pattern that will be used to fetch files. Checks that the pattern is valid and that at least one file is found.", "enum": [ "file-path", "directory-path", @@ -163,15 +165,15 @@ "type": "string", "format": "regex", "minLength": 1, - "description": "Check a parameter value of 'string' type against a regex pattern" + "description": "Regular expression which the string must match in order to pass validation.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#regular-expressions)\n for details.\n- Use for help with writing regular expressions.\n\nFor example, this pattern only validates if the supplied string ends in `.fastq`, `.fq`, `.fastq.gz` or `.fq.gz`:\n\n```json\n{\n \"type\": \"string\",\n \"pattern\": \".*.f(ast)?q(.gz)?$\"\n}\n```" }, "description": { "type": "string", - "description": "The description of the current parameter" + "description": "A short description of what the parameter does, written in markdown.\nPrinted in docs and terminal help text.\nShould be maximum one short sentence." }, "default": { "$ref": "#/$defs/allTypes", - "description": "Specifies a default value to use for this parameter" + "description": "Default value for the parameter.\n\nShould match the `type` and validation patterns set for the parameter in other fields.\n\n!!! tip\n\n If no default should be set, completely omit this key from the schema.\n Do not set it as an empty string, or `null`.\n\n However, parameters with no defaults _should_ be set to `null` within your Nextflow config file.\n\n!!! note\n\n When creating a schema using `nf-core schema build`, this field will be automatically created based\n on the default value defined in the pipeline config files.\n\n Generally speaking, the two should always be kept in sync to avoid unexpected problems and usage errors.\n In some rare cases, this may not be possible (for example, a dynamic groovy expression cannot be encoded in JSON),\n in which case try to specify as \"sensible\" a default within the schema as possible." }, "examples": { "type": "array", @@ -182,31 +184,31 @@ }, "deprecated": { "type": "boolean", - "description": "States that the parameter is deprecated. Please provide a nice deprecation message using 'errorMessage'" + "description": "!!! example \"Extended key\"\n\nA boolean JSON flag that instructs anything using the schema that this parameter/field is deprecated and should not be used. This can be useful to generate messages telling the user that a parameter has changed between versions.\n\nJSON schema states that this is an informative key only, but in [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) this will cause a validation error if the parameter/field is used.\n\n!!! tip\n\n Using the [`errorMessage`](#errormessage) keyword can be useful to provide more information about the deprecation and what to use instead." }, "minLength": { "$ref": "#/$defs/nonNegativeInteger", - "description": "The minimum length a 'string' parameter value should be" + "description": "Specify a minimum / maximum string length with `minLength` and `maxLength`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#length)\n for details.\n\n```json\n{\n \"type\": \"string\",\n \"minLength\": 2,\n \"maxLength\": 3\n}\n```" }, "maxLength": { "$ref": "#/$defs/nonNegativeInteger", - "description": "The maximum length a 'string' parameter value should be" + "description": "Specify a minimum / maximum string length with `minLength` and `maxLength`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/string.html#length)\n for details.\n\n```json\n{\n \"type\": \"string\",\n \"minLength\": 2,\n \"maxLength\": 3\n}\n```" }, "minimum": { "type": "number", - "description": "The mimimum value an 'integer' or 'number' parameter value should be" + "description": "Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range)\n for details.\n\n> If x is the value being validated, the following must hold true:\n>\n> - `x` ≥ `minimum`\n> - `x` ≤ `maximum`\n\n```json\n{\n \"type\": \"number\",\n \"minimum\": 0,\n \"maximum\": 100\n}\n```\n\n!!! note\n\n The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys.\n Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys.\n However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them." }, "exclusiveMinimum": { "type": "number", - "description": "The exclusive mimimum value an 'integer' or 'number' parameter value should be" + "description": "Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range)\n for details.\n\n> If x is the value being validated, the following must hold true:\n>\n> - `x` ≥ `minimum`\n> - `x` ≤ `maximum`\n\n```json\n{\n \"type\": \"number\",\n \"minimum\": 0,\n \"maximum\": 100\n}\n```\n\n!!! note\n\n The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys.\n Because [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) uses stock JSON schema validation libraries, these _should_ work for validating keys.\n However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them." }, "maximum": { "type": "number", - "description": "The maximum value an 'integer' or 'number' parameter value should be" + "description": "Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range)\n for details.\n\n> If x is the value being validated, the following must hold true:\n>\n> - `x` ≥ `minimum`\n> - `x` ≤ `maximum`\n\n```json\n{\n \"type\": \"number\",\n \"minimum\": 0,\n \"maximum\": 100\n}\n```\n\n!!! note\n\n The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys.\n Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys.\n However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them." }, "exclusiveMaximum": { "type": "number", - "description": "The exclusive maximum value an 'integer' or 'number' parameter value should be" + "description": "Specify a minimum / maximum value for an integer or float number length with `minimum` and `maximum`.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/numeric.html#range)\n for details.\n\n> If x is the value being validated, the following must hold true:\n>\n> - `x` ≥ `minimum`\n> - `x` ≤ `maximum`\n\n```json\n{\n \"type\": \"number\",\n \"minimum\": 0,\n \"maximum\": 100\n}\n```\n\n!!! note\n\n The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys.\n Because nf-schema uses stock JSON schema validation libraries, these _should_ work for validating keys.\n However, they are not officially supported within the Nextflow schema ecosystem and so some interfaces may not recognise them." }, "multipleOf": { "type": "number", @@ -218,7 +220,7 @@ "items": { "$ref": "#/$defs/allTypes" }, - "description": "The parameter value should be one of the values specified in this enum array" + "description": "An array of enumerated values: the parameter must match one of these values exactly to pass validation.\n\n- See the [JSON schema docs](https://json-schema.org/understanding-json-schema/reference/generic.html#enumerated-values)\n for details.\n- Available for strings, numbers and integers.\n\n```json\n{\n \"enum\": [\"red\", \"amber\", \"green\"]\n}\n```" }, "const": { "$ref": "#/$defs/allTypes", @@ -233,34 +235,34 @@ "errorMessage": { "type": "string", "minLength": 1, - "description": "NON STANDARD OPTION: The custom error message to display in case validation against this parameter fails. Can also be used as a deprecation message if 'deprecated' is true" + "description": "\n!!! example \"Non-standard key\"\n\nIf validation fails, an error message is printed to the terminal, so that the end user knows what to fix.\nHowever, these messages are not always very clear - especially to newcomers.\n\nTo improve this experience, pipeline developers can set a custom `errorMessage` for a given parameter in a the schema.\nIf validation fails, this `errorMessage` is printed after the original error message to guide the pipeline users to an easier solution.\n\nFor example, instead of printing:\n\n```\n* --input (samples.yml): \"samples.yml\" does not match regular expression [^\\S+\\.csv$]\n```\n\nWe can set\n\n```json\n\"input\": {\n \"type\": \"string\",\n \"pattern\": \"^\\S+\\.csv$\",\n \"errorMessage\": \"File name must end in '.csv' cannot contain spaces\"\n}\n```\n\nand get:\n\n```\n* --input (samples.yml): \"samples.yml\" does not match regular expression [^\\S+\\.csv$] (File name must end in '.csv' cannot contain spaces)\n```" }, "exists": { "type": "boolean", - "description": "NON STANDARD OPTION: Check if a file exists. This parameter value needs to be a `string` type with one of these formats: `['path', 'file-path', 'directory-path', 'file-path-pattern']`" + "description": "When a format is specified for a value, you can provide the key `exists` set to true in order to validate that the provided path exists. Set this to `false` to validate that the path does not exist.\n\nExample usage is as follows:\n\n```json\n{\n \"type\": \"string\",\n \"format\": \"file-path\",\n \"exists\": true\n}\n```\n\n!!! note\n\n If the parameter is an S3, Azure or Google Cloud URI path, this validation is ignored.\n\n!!! warning\n\n Make sure to only use the `exists` keyword in combination with any file path format. Using `exists` on a normal string will assume that it's a file and will probably fail unexpectedly." }, "schema": { "type": "string", "minLength": 1, "pattern": "\\.json$", - "description": "NON STANDARD OPTION: Check the given file against a schema passed to this keyword. Will only work when type is `string` and format is `path` or `file-path`" + "description": "Path to a JSON schema file used to validate _the supplied file_.\n\nShould only be set when `format` is `file-path`.\n\n!!! tip\n\n Setting this field is key to working with sample sheet validation and channel generation, as described in the sample sheet section of the [nf-schema docs](https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/sample_sheet_schema_specification/).\n\nThese schema files are typically stored in the pipeline `assets` directory, but can be anywhere.\n\n```json\n{\n \"type\": \"string\",\n \"format\": \"file-path\",\n \"schema\": \"assets/foo_schema.json\"\n}\n```\n\n!!! note\n\n If the parameter is set to `null`, `false` or an empty string, this validation is ignored. The file won't be validated." }, "help_text": { "type": "string", - "description": "NON STANDARD OPTION: A more detailed help text" + "description": "\n!!! example \"Non-standard key\"\n\nA longer text with usage help for the parameter, written in markdown.\nCan include newlines with multiple paragraphs and more complex markdown structures.\n\nTypically hidden by default in documentation and interfaces, unless explicitly clicked / requested." }, "fa_icon": { "type": "string", "pattern": "^fa", - "description": "NON STANDARD OPTION: A font awesome icon to use in the nf-core parameter documentation" + "description": "\n!!! example \"Non-standard key\"\n\nA text identifier corresponding to an icon from [Font Awesome](https://fontawesome.com/).\nUsed for easier visual navigation of documentation and pipeline interfaces.\n\nShould be the font-awesome class names, for example:\n\n```json\n\"fa_icon\": \"fas fa-file-csv\"\n```" }, "hidden": { "type": "boolean", - "description": "NON STANDARD OPTION: Hide this parameter from the help message and documentation" + "description": "\n!!! example \"Non-standard key\"\n\nA boolean JSON flag that instructs anything using the schema that this is an unimportant parameter.\n\nTypically used to keep the pipeline docs / UIs uncluttered with common parameters which are not used by the majority of users.\nFor example, `--plaintext_email` and `--monochrome_logs`.\n\n```json\n\"hidden\": true\n```" }, "mimetype": { "type": "string", - "description": "NON STANDARD OPTION: The MIME type of the parameter value", + "description": "MIME type for a file path. Setting this value informs downstream tools about what _kind_ of file is expected.\n\nShould only be set when `format` is `file-path`.\n\n- See a [list of common MIME types](https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types)\n\n```json\n{\n \"type\": \"string\",\n \"format\": \"file-path\",\n \"mimetype\": \"text/csv\"\n}\n```", "deprecated": true, "errorMessage": "The 'mimetype' keyword is deprecated. 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head and should contain a +# meaningful description of the site content for use by search engines. +# +# Read more: https://zensical.org/docs/setup/basics/#site_description +site_description = "Specifications of Nextflow schemas" + +# The site_author attribute. This is used in the HTML head element. +# +# Read more: https://zensical.org/docs/setup/basics/#site_author +site_author = "Matthias Hörtenhuber" + +# The site_url is the canonical URL for your site. When building online +# documentation you should set this. +# Read more: https://zensical.org/docs/setup/basics/#site_url +#site_url = "https://www.example.com/" + +# The copyright notice appears in the page footer and can contain an HTML +# fragment. +# +# Read more: https://zensical.org/docs/setup/basics/#copyright +copyright = """ +Copyright © 2026 The authors +""" + +repo_url = "https://github.com/nextflow-io/schemas" +repo_name = "nextflow-io/schemas" + +# Zensical supports both implicit navigation and explicitly defined navigation. +# If you decide not to define a navigation here then Zensical will simply +# derive the navigation structure from the directory structure of your +# "docs_dir". The definition below demonstrates how a navigation structure +# can be defined using TOML syntax. +# +# Read more: https://zensical.org/docs/setup/navigation/ +# nav = [ +# { "Get started" = "index.md" }, +# { "Markdown in 5min" = "markdown.md" }, +# ] + +# With the "extra_css" option you can add your own CSS styling to customize +# your Zensical project according to your needs. You can add any number of +# CSS files. +# +# The path provided should be relative to the "docs_dir". +# +# Read more: https://zensical.org/docs/customization/#additional-css +# +extra_css = ["stylesheets/extra.css"] + +# With the `extra_javascript` option you can add your own JavaScript to your +# project to customize the behavior according to your needs. +# +# The path provided should be relative to the "docs_dir". +# +# Read more: https://zensical.org/docs/customization/#additional-javascript +#extra_javascript = ["javascripts/extra.js"] + +# ---------------------------------------------------------------------------- +# Section for configuring theme options +# ---------------------------------------------------------------------------- +[project.theme] + +# change this to "classic" to use the traditional Material for MkDocs look. +#variant = "classic" + +# Zensical allows you to override specific blocks, partials, or whole +# templates as well as to define your own templates. To do this, uncomment +# the custom_dir setting below and set it to a directory in which you +# keep your template overrides. +# +# Read more: +# - https://zensical.org/docs/customization/#extending-the-theme +# +#custom_dir = "overrides" + +# With the "favicon" option you can set your own image to use as the icon +# browsers will use in the browser title bar or tab bar. The path provided +# must be relative to the "docs_dir". +# +# Read more: +# - https://zensical.org/docs/setup/logo-and-icons/#favicon +# - https://developer.mozilla.org/en-US/docs/Glossary/Favicon +# +#favicon = "images/favicon.png" + +# Zensical supports more than 60 different languages. This means that the +# labels and tooltips that Zensical's templates produce are translated. +# The "language" option allows you to set the language used. This language +# is also indicated in the HTML head element to help with accessibility +# and guide search engines and translation tools. +# +# The default language is "en" (English). It is possible to create +# sites with multiple languages and configure a language selector. See +# the documentation for details. +# +# Read more: +# - https://zensical.org/docs/setup/language/ +# +language = "en" + +# Zensical provides a number of feature toggles that change the behavior +# of the documentation site. +features = [ + # Zensical includes an announcement bar. This feature allows users to + # dismiss it then they have read the announcement. + # https://zensical.org/docs/setup/header/#announcement-bar + "announce.dismiss", + + # If you have a repository configured and turn on this feature, Zensical + # will generate an edit button for the page. This works for common + # repository hosting services. + # https://zensical.org/docs/setup/repository/#code-actions + "content.action.edit", + + # If you have a repository configured and turn on this feature, Zensical + # will generate a button that allows the user to view the Markdown + # code for the current page. + # https://zensical.org/docs/setup/repository/#code-actions + #"content.action.view", + + # Code annotations allow you to add an icon with a tooltip to your + # code blocks to provide explanations at crucial points. + # https://zensical.org/docs/authoring/code-blocks/#code-annotations + "content.code.annotate", + + # This feature turns on a button in code blocks that allow users to + # copy the content to their clipboard without first selecting it. + # https://zensical.org/docs/authoring/code-blocks/#code-copy-button + "content.code.copy", + + # Code blocks can include a button to allow for the selection of line + # ranges by the user. + # https://zensical.org/docs/authoring/code-blocks/#code-selection-button + "content.code.select", + + # Zensical can render footnotes as inline tooltips, so the user can read + # the footnote without leaving the context of the document. + # https://zensical.org/docs/authoring/footnotes/#footnote-tooltips + "content.footnote.tooltips", + + # If you have many content tabs that have the same titles (e.g., "Python", + # "JavaScript", "Cobol"), this feature causes all of them to switch to + # at the same time when the user chooses their language in one. + # https://zensical.org/docs/authoring/content-tabs/#linked-content-tabs + "content.tabs.link", + + # TODO: not sure I understand this one? Is there a demo of this in the docs? + # https://zensical.org/docs/authoring/tooltips/#improved-tooltips + "content.tooltips", + + # With this feature enabled, Zensical will automatically hide parts + # of the header when the user scrolls past a certain point. + # https://zensical.org/docs/setup/header/#automatic-hiding + # "header.autohide", + + # Turn on this feature to expand all collapsible sections in the + # navigation sidebar by default. + # https://zensical.org/docs/setup/navigation/#navigation-expansion + # "navigation.expand", + + # This feature turns on navigation elements in the footer that allow the + # user to navigate to a next or previous page. + # https://zensical.org/docs/setup/footer/#navigation + "navigation.footer", + + # When section index pages are enabled, documents can be directly attached + # to sections, which is particularly useful for providing overview pages. + # https://zensical.org/docs/setup/navigation/#section-index-pages + "navigation.indexes", + + # When instant navigation is enabled, clicks on all internal links will be + # intercepted and dispatched via XHR without fully reloading the page. + # https://zensical.org/docs/setup/navigation/#instant-navigation + "navigation.instant", + + # With instant prefetching, your site will start to fetch a page once the + # user hovers over a link. This will reduce the perceived loading time + # for the user. + # https://zensical.org/docs/setup/navigation/#instant-prefetching + "navigation.instant.prefetch", + + # In order to provide a better user experience on slow connections when + # using instant navigation, a progress indicator can be enabled. + # https://zensical.org/docs/setup/navigation/#progress-indicator + #"navigation.instant.progress", + + # When navigation paths are activated, a breadcrumb navigation is rendered + # above the title of each page + # https://zensical.org/docs/setup/navigation/#navigation-path + "navigation.path", + + # When pruning is enabled, only the visible navigation items are included + # in the rendered HTML, reducing the size of the built site by 33% or more. + # https://zensical.org/docs/setup/navigation/#navigation-pruning + #"navigation.prune", + + # When sections are enabled, top-level sections are rendered as groups in + # the sidebar for viewports above 1220px, but remain as-is on mobile. + # https://zensical.org/docs/setup/navigation/#navigation-sections + "navigation.sections", + + # When tabs are enabled, top-level sections are rendered in a menu layer + # below the header for viewports above 1220px, but remain as-is on mobile. + # https://zensical.org/docs/setup/navigation/#navigation-tabs + "navigation.tabs", + + # When sticky tabs are enabled, navigation tabs will lock below the header + # and always remain visible when scrolling down. + # https://zensical.org/docs/setup/navigation/#sticky-navigation-tabs + "navigation.tabs.sticky", + + # A back-to-top button can be shown when the user, after scrolling down, + # starts to scroll up again. + # https://zensical.org/docs/setup/navigation/#back-to-top-button + "navigation.top", + + # When anchor tracking is enabled, the URL in the address bar is + # automatically updated with the active anchor as highlighted in the table + # of contents. + # https://zensical.org/docs/setup/navigation/#anchor-tracking + "navigation.tracking", + + # When search highlighting is enabled and a user clicks on a search result, + # Zensical will highlight all occurrences after following the link. + # https://zensical.org/docs/setup/search/#search-highlighting + "search.highlight", + + # When anchor following for the table of contents is enabled, the sidebar + # is automatically scrolled so that the active anchor is always visible. + # https://zensical.org/docs/setup/navigation/#anchor-following + "toc.follow", + + # When navigation integration for the table of contents is enabled, it is + # always rendered as part of the navigation sidebar on the left. + # https://zensical.org/docs/setup/navigation/#navigation-integration + #"toc.integrate", +] + +# ---------------------------------------------------------------------------- +# In the "palette" subsection you can configure options for the color scheme. +# You can configure different color # schemes, e.g., to turn on dark mode, +# that the user can switch between. Each color scheme can be further +# customized. +# +# Read more: +# - https://zensical.org/docs/setup/colors/ +# ---------------------------------------------------------------------------- +# Palette toggle for automatic mode +[[project.theme.palette]] +media = "(prefers-color-scheme)" +toggle.icon = "lucide/eye" +toggle.name = "Switch to light mode" + +# Palette toggle for light mode +[[project.theme.palette]] +media = "(prefers-color-scheme: light)" +scheme = "default" +toggle.icon = "lucide/sun" +toggle.name = "Switch to dark mode" + +# Palette toggle for dark mode +[[project.theme.palette]] +media = "(prefers-color-scheme: dark)" +scheme = "slate" +toggle.icon = "lucide/moon" +toggle.name = "Switch to system preference" + +# ---------------------------------------------------------------------------- +# In the "font" subsection you can configure the fonts used. By default, fonts +# are loaded from Google Fonts, giving you a wide range of choices from a set +# of suitably licensed fonts. There are options for a normal text font and for +# a monospaced font used in code blocks. +# ---------------------------------------------------------------------------- +[project.theme.font] +text = "Inter" +code = "Fira Code" + +# ---------------------------------------------------------------------------- +# You can configure your own logo to be shown in the header using the "logo" +# option in the "icons" subsection. The logo can be a path to a file in your +# "docs_dir" or it can be a path to an icon. +# +# Likewise, you can customize the logo used for the repository section of the +# header. Zensical derives the default logo for this from the repository URL. +# See below... +# +# There are other icons you can customize. See the documentation for details. +# +# Read more: +# - https://zensical.org/docs/setup/logo-and-icons +# - https://zensical.org/docs/authoring/icons-emojis/#search +# ---------------------------------------------------------------------------- +[project.theme.icon] +logo = "lucide/braces" +#repo = "lucide/smile" + +# ---------------------------------------------------------------------------- +# The "extra" section contains miscellaneous settings. +# ---------------------------------------------------------------------------- +#[[project.extra.social]] +#icon = "fontawesome/brands/github" +#link = "https://github.com/user/repo"