rebrand nf-validation to nf-schema

.github/workflows/build-docs.yml

@@ -19,7 +19,7 @@ jobs:
           python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - name: Obtain version from MANIFEST.MF
-        run: echo "plugin_version=$(grep "Plugin-Version" plugins/nf-validation/src/resources/META-INF/MANIFEST.MF | awk '{print $2}' | awk -F '.' '{print $1"."$2}')" >> $GITHUB_ENV
+        run: echo "plugin_version=$(grep "Plugin-Version" plugins/nf-schema/resources/META-INF/MANIFEST.MF | awk '{print $2}' | awk -F '.' '{print $1"."$2}')" >> $GITHUB_ENV
       - name: Setup git user
         run: |
           git config --global user.name "${{github.actor}}"

.github/workflows/build.yml

@@ -51,4 +51,4 @@ jobs:
         with:
           name: test-reports-jdk-${{ matrix.java_version }}
           path: |
-            ./plugins/nf-validation/build/reports/tests/test/**
+            ./plugins/nf-schema/build/reports/tests/test/**

CHANGELOG.md

@@ -1,4 +1,4 @@
-# nextflow-io/nf-validation: Changelog
+# nextflow-io/nf-schema: Changelog
 
 # Version 2.0.0 - Kagoshima
 

README.md

@@ -1,6 +1,6 @@
-# ![nf-validation](docs/images/nf-validation.svg)
+# ![nf-schema](docs/images/nf-schema.svg)
 
-## 📚 Docs 👉🏻 <https://nextflow-io.github.io/nf-validation>
+## 📚 Docs 👉🏻 <https://nextflow-io.github.io/nf-schema>
 
 **A Nextflow plugin to work with validation of pipeline parameters and sample sheets.**
 
@@ -22,7 +22,7 @@ Declare the plugin in your Nextflow pipeline configuration file:
 
 ```groovy title="nextflow.config"
 plugins {
-  id 'nf-validation'
+  id 'nf-schema'
 }
 ```
 
@@ -31,12 +31,12 @@ This is all that is needed - Nextflow will automatically fetch the plugin code a
 > [!NOTE]
 > The snippet above will always try to install the latest version, good to make sure
 > that the latest bug fixes are included! However, this can cause difficulties if running
-> offline. You can pin a specific release using the syntax `nf-validation@2.0.0`
+> offline. You can pin a specific release using the syntax `nf-schema@2.0.0`
 
 You can now include the plugin helper functions into your Nextflow pipeline:
 
 ```groovy title="main.nf"
-include { validateParameters; paramsHelp; paramsSummaryLog; fromSamplesheet } from 'plugin/nf-validation'
+include { validateParameters; paramsHelp; paramsSummaryLog; fromSamplesheet } from 'plugin/nf-schema'
 
 // Print help message, supply typical command line usage for the pipeline
 if (params.help) {

docs/background.md

@@ -1,6 +1,6 @@
 ---
 title: Background
-description: Get up and running with nf-validation
+description: Get up and running with nf-schema
 hide:
   - toc
 ---
@@ -14,4 +14,4 @@ In addition to config params, a common best-practice for pipelines is to use a "
 
 Nextflow itself does not provide functionality to validate config parameters or parsed sample sheets. To bridge this gap, we developed code within the [nf-core community](https://nf-co.re/) to allow pipelines to work with a standard `nextflow_schema.json` file, written using the [JSON Schema](https://json-schema.org/) format. The file allows strict typing of parameter variables and inclusion of validation rules.
 
-The nf-validation plugin moves this code out of the nf-core template into a stand-alone package, to make it easier to use for the wider Nextflow community. It also incorporates a number of new features, such as native Groovy sample sheet validation.
+The nf-schema plugin moves this code out of the nf-core template into a stand-alone package, to make it easier to use for the wider Nextflow community. It also incorporates a number of new features, such as native Groovy sample sheet validation.

docs/contributing/setup.md

@@ -1,6 +1,6 @@
 ---
 title: Contribution instructions
-description: How to contribute to nf-validation
+description: How to contribute to nf-schema
 ---
 
 # Getting started with plugin development
@@ -39,7 +39,7 @@ Compile the plugin code
 Run nextflow with this command:
 
 ```bash
-./launch.sh run -plugins nf-validation <script/pipeline name> [pipeline params]
+./launch.sh run -plugins nf-schema <script/pipeline name> [pipeline params]
 ```
 
 ## Change and preview the docs
@@ -51,7 +51,7 @@ You can install the required packages as follows:
 pip install mkdocs-material pymdown-extensions pillow cairosvg
 ```
 
-To change the docs, edit the files in the [docs/](https://github.com/nextflow-io/nf-validation/tree/master/docs) folder and run the following command to generate the docs:
+To change the docs, edit the files in the [docs/](https://github.com/nextflow-io/nf-schema/tree/master/docs) folder and run the following command to generate the docs:
 
 ```bash
 mkdocs serve

docs/index.md

@@ -1,9 +1,9 @@
 ---
-title: nf-validation
+title: nf-schema
 description: Nextflow plugin for sample sheet validation
 ---
 
-# ![nf-validation](images/nf-validation.svg)
+# ![nf-schemaages/nf-scheschemg
 
 {==
 

docs/migration_guide.md

@@ -1,6 +1,6 @@
 ---
 title: Migration guide
-description: Guide to migrate pipelines using nf-validation pre v2.0.0 to after v2.0.0
+description: Guide to migrate pipelines using nf-schema pre v2.0.0 to after v2.0.0
 hide:
   - toc
 ---
@@ -17,7 +17,7 @@ Following list shows the major breaking changes introduced in version 2.0.0:
 2. The `unique` keyword for samplesheet schemas has been removed. Please use [`uniqueItems`](https://json-schema.org/understanding-json-schema/reference/array#uniqueItems) or [`uniqueEntries`](nextflow_schema/nextflow_schema_specification.md#uniqueentries) now instead.
 3. The `dependentRequired` keyword now works as it's supposed to work in JSON schema. See [`dependentRequired`](https://json-schema.org/understanding-json-schema/reference/conditionals#dependentRequired) for more information
 
-A full list of changes can be found in the [changelog](https://github.com/nextflow-io/nf-validation/blob/master/CHANGELOG.md).
+A full list of changes can be found in the [changelog](https://github.com/nextflow-io/nf-schema/blob/master/CHANGELOG.md).
 
 ## Updating your pipeline
 

docs/nextflow_schema/create_schema.md

@@ -48,7 +48,7 @@ nf-core schema build
 
 !!! warning
 
-    The current version of `nf-core` tools (v2.12.1) does not support the new schema draft used in `nf-validation`. Running this command after building the schema will convert the schema to the right draft:
+    The current version of `nf-core` tools (v2.12.1) does not support the new schema draft used in `nf-schemaunning this command after building the schema will convert the schema to the right draft:
 
     ```bash
     sed -i -e 's/http:\/\/json-schema.org\/draft-07\/schema/https:\/\/json-schema.org\/draft\/2020-12\/schema/g' -e 's/definitions/defs/g' nextflow_schema.json

docs/nextflow_schema/index.md

@@ -1,11 +1,11 @@
 ---
 title: Introduction
-description: Introduction to the nf-validation plugin
+description: Introduction to the nf-schema plugin
 ---
 
 # Nextflow schema for parameters
 
-The functionality of the nf-validation plugin centres on a pipeline _schema_ file.
+The functionality of the nf-schema plugin centres on a pipeline _schema_ file.
 By convention, this file is stored in the workflow root directory and called `nextflow_schema.json`.
 
 ## What it does

docs/nextflow_schema/nextflow_schema_examples.md

@@ -9,12 +9,12 @@ hide:
 You can see an example JSON Schema for a Nextflow pipeline `nextflow_schema.json` file below.
 
 This file was generated from the nf-core pipeline template, using `nf-core create`.
-It is used as a test fixture in the nf-validation package [here](https://github.com/nextflow-io/nf-validation/blob/master/plugins/nf-validation/src/testResources/nextflow_schema.json).
+It is used as a test fixture in the nf-schemakage [here](https://github.com/nextflow-io/nf-snf-schemaster/plugins/nf-schemnf-schemaources/nextflow_schema.json).
 
 !!! note
 
-    More examples can be found in the plugin [`testResources` directory](https://github.com/nextflow-io/nf-validation/blob/master/plugins/nf-validation/src/testResources/).
+    More examples can be found in the plugin [`testResources` directory](https://github.com/nextflow-io/nf-schemab/master/plugins/nf-snf-schematResources/).
 
 ```json
---8<-- "plugins/nf-validation/src/testResources/nextflow_schema.json"
+--8<-- "plugins/nf-schema/testResources/nextflow_schema.json"
 ```

docs/nextflow_schema/nextflow_schema_specification.md

@@ -22,7 +22,7 @@ You can find more information about JSON Schema here:
 
 !!! note
 
-    The nf-validation plugin, as well as several other interfaces using Nextflow schema, uses a stock JSON schema library for parameter validation.
+    The nf-schema plugin, as well as several other interfaces using Nextflow schema, uses a stock JSON schema library for parameter validation.
     As such, any valid JSON schema _should_ work for validation.
 
     However, please note that graphical UIs (docs, launch interfaces) are largely hand-written and may not expect JSON schema usage that is
@@ -247,7 +247,7 @@ and get:
 
 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-validation` this will cause a validation error if the parameter/field is used.
+JSON schema states that this is an informative key only, but in `nf-schema` this will cause a validation error if the parameter/field is used.
 
 !!! tip
 
@@ -401,7 +401,7 @@ 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 next section of the nf-validation docs.
+    Setting this field is key to working with sample sheet validation and channel generation, as described in the next section of the nf-schema docs.
 
 These schema files are typically stored in the pipeline `assets` directory, but can be anywhere.
 
@@ -442,7 +442,7 @@ Specify a minimum / maximum value for an integer or float number length with `mi
 !!! note
 
     The JSON schema doc also mention `exclusiveMinimum`, `exclusiveMaximum` and `multipleOf` keys.
-    Because nf-validation uses stock JSON schema validation libraries, these _should_ work for validating 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.
 
 ## Array-specific keys
@@ -481,4 +481,4 @@ The combination of all values in the given keys should be unique. For this key t
 }
 ```
 
-This schema tells `nf-validation` that the combination of `foo` and `bar` should be unique across all objects in the array.
+This schema tells `nf-schema` that the combination of `foo` and `bar` should be unique across all objects in the array.

docs/nextflow_schema/sample_sheet_schema_examples.md

@@ -58,16 +58,16 @@ You can see this, used for validating sample sheets with `--input` here: [`asset
 }
 ```
 
-## nf-validation test case
+## nf-schema test case
 
 You can see a very feature-complete example JSON Schema for a sample sheet schema file below.
 
-It is used as a test fixture in the nf-validation package [here](https://github.com/nextflow-io/nf-validation/blob/master/plugins/nf-validation/src/testResources/schema_input.json).
+It is used as a test fixture in the nf-schema package [here](https://github.com/nextflow-io/nf-schema/blob/master/plugins/nf-schema/src/testResources/schema_input.json).
 
 !!! note
 
-    More examples can be found in the plugin [`testResources` directory](https://github.com/nextflow-io/nf-validation/blob/master/plugins/nf-validation/src/testResources/).
+    More examples can be found in the plugin [`testResources` directory](https://github.com/nextflow-io/nf-schema/blob/master/plugins/nf-schema/src/testResources/).
 
 ```json
---8<-- "plugins/nf-validation/src/testResources/schema_input.json"
+--8<-- "plugins/nf-schema/src/testResources/schema_input.json"
 ```

docs/nextflow_schema/sample_sheet_schema_specification.md

@@ -4,7 +4,7 @@ description: Schema specification for sample sheet validation
 
 # Sample sheet schema specification
 
-Sample sheet schema files are used by the nf-validation plugin for validation of sample sheet contents and type conversion / channel generation.
+Sample sheet schema files are used by the nf-schemagin for validation of sample sheet contents and type conversion / channel generation.
 
 The Nextflow schema syntax is based on the JSON schema standard.
 You can find more information about JSON Schema here:
@@ -94,4 +94,4 @@ For example:
 ```
 
 will convert the `field` value to a meta value, resulting in the channel `[[id:value]...]`
-See [here](https://github.com/nextflow-io/nf-validation/blob/ce3aef60e5103ea4798375fe6c59bae41b7d2a25/plugins/nf-validation/src/testResources/schema_input.json#L10-L25) for an example in the sample sheet.
+See [here](https://github.com/nextflow-io/nf-schemab/ce3aef60e5103ea4798375fe6c59bae41b7d2a25/plugins/nf-scheschemctResources/schema_input.json#L10-L25) for an example in the sample sheet.

docs/samplesheets/examples.md

@@ -7,7 +7,7 @@ description: Examples of advanced sample sheet creation techniques.
 
 ## Introduction
 
-Understanding channel structure and manipulation is critical for getting the most out of Nextflow. nf-validation helps initialise your channels from the text inputs to get you started, but further work might be required to fit your exact use case. In this page we run through some common cases for transforming the output of `.fromSamplesheet`.
+Understanding channel structure and manipulation is critical for getting the most out of Nextflow. nf-schema helps initialise your channels from the text inputs to get you started, but further work might be required to fit your exact use case. In this page we run through some common cases for transforming the output of `.fromSamplesheet`.
 
 ### Glossary
 

docs/samplesheets/fromSamplesheet.md

@@ -35,7 +35,7 @@ Channel.fromSamplesheet('input', parameters_schema: 'custom_nextflow_schema.json
 
 ## Basic example
 
-In [this example](https://github.com/nextflow-io/nf-validation/tree/master/examples/fromSamplesheetBasic), we create a simple channel from a CSV sample sheet.
+In [this example](https://github.com/nextflow-io/nf-schema/tree/master/examples/fromSamplesheetBasic), we create a simple channel from a CSV sample sheet.
 
 ```
 --8<-- "examples/fromSamplesheetBasic/log.txt"
@@ -73,7 +73,7 @@ In [this example](https://github.com/nextflow-io/nf-validation/tree/master/examp
 
 ## Order of fields
 
-[This example](https://github.com/nextflow-io/nf-validation/tree/master/examples/fromSamplesheetOrder) demonstrates that the order of columns in the sample sheet file has no effect.
+[This example](https://github.com/nextflow-io/nf-schema/tree/master/examples/fromSamplesheetOrder) demonstrates that the order of columns in the sample sheet file has no effect.
 
 !!! danger
 
@@ -115,7 +115,7 @@ In [this example](https://github.com/nextflow-io/nf-validation/tree/master/examp
 
 ## Channel with meta map
 
-In [this example](https://github.com/nextflow-io/nf-validation/tree/master/examples/fromSamplesheetMeta), we use the schema to mark two columns as meta fields.
+In [this example](https://github.com/nextflow-io/nf-schema/tree/master/examples/fromSamplesheetMeta), we use the schema to mark two columns as meta fields.
 This returns a channel with a meta map.
 
 ```

docs/samplesheets/validate_sample_sheet.md

@@ -10,7 +10,7 @@ parse and validate the provided file contents using this JSON schema.
 It can validate CSV, TSV, JSON and YAML files.
 
 The path of the schema file must be relative to the root of the pipeline directory.
-See an example in the `input` field from the [example schema.json](https://raw.githubusercontent.com/nextflow-io/nf-validation/master/plugins/nf-validation/src/testResources/nextflow_schema_with_samplesheet.json#L20).
+See an example in the `input` field from the [example schema.json](https://raw.githubusercontent.com/nextflow-io/nf-schema/master/plugins/nf-schema/src/testResources/nextflow_schema_with_samplesheet.json#L20).
 
 ```json
 {

docs/schema_input.json

@@ -1,6 +1,6 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://raw.githubusercontent.com/nextflow-io/nf-validation/master/plugins/nf-validation/src/testResources/schema_input.json",
+  "$id": "https://raw.githubusercontent.com/nextflow-io/nf-schemater/plugins/nf-snf-schematResources/schema_input.json",
   "title": "Samplesheet validation schema",
   "description": "Schema for the samplesheet used in this pipeline",
   "type": "object",

examples/fromSamplesheetBasic/pipeline/assets/schema_input.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://raw.githubusercontent.com/nf-validation/example/master/assets/schema_input.json",
-  "title": "nf-validation example - params.input schema",
+  "$id": "https://raw.githubusercontent.com/nf-schema/example/master/assets/schema_input.json",
+  "title": "nf-schema example - params.input schema",
   "description": "Schema for the file provided with params.input",
   "type": "array",
   "items": {

examples/fromSamplesheetBasic/pipeline/main.nf

@@ -1,4 +1,4 @@
-include { fromSamplesheet } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-schema'
 
 ch_input = Channel.fromSamplesheet("input")
 

examples/fromSamplesheetBasic/pipeline/nextflow.config

@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-validation@2.0.0'
+  id 'nf-schema@2.0.0'
 }
 
 params {

examples/fromSamplesheetMeta/pipeline/assets/schema_input.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://raw.githubusercontent.com/nf-validation/example/master/assets/schema_input.json",
-  "title": "nf-validation example - params.input schema",
+  "$id": "https://raw.githubusercontent.com/nf-schemample/master/assets/schema_input.json",
+  "title": "nf-schemample - params.input schema",
   "description": "Schema for the file provided with params.input",
   "type": "array",
   "items": {

examples/fromSamplesheetMeta/pipeline/main.nf

@@ -1,4 +1,4 @@
-include { fromSamplesheet } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-schema'
 
 ch_input = Channel.fromSamplesheet("input")
 

examples/fromSamplesheetMeta/pipeline/nextflow.config

@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-validation@2.0.0'
+  id 'nf-schema@2.0.0'
 }
 
 params {

examples/fromSamplesheetOrder/pipeline/assets/schema_input.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "$id": "https://raw.githubusercontent.com/nf-validation/example/master/assets/schema_input.json",
-  "title": "nf-validation example - params.input schema",
+  "$id": "https://raw.githubusercontent.com/nf-schema/example/master/assets/schema_input.json",
+  "title": "nf-schema example - params.input schema",
   "description": "Schema for the file provided with params.input",
   "type": "array",
   "items": {

examples/fromSamplesheetOrder/pipeline/main.nf

@@ -1,4 +1,4 @@
-include { fromSamplesheet } from 'plugin/nf-validation'
+include { fromSamplesheet } from 'plugin/nf-schema'
 
 ch_input = Channel.fromSamplesheet("input")
 

examples/fromSamplesheetOrder/pipeline/nextflow.config

@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-[email protected].0'
+  id 'nf-schema.0'
 }
 
 params {

examples/paramsHelp/pipeline/main.nf

@@ -1,4 +1,4 @@
-include { paramsHelp } from 'plugin/nf-validation'
+include { paramsHelp } from 'plugin/nf-schema'
 
 if (params.help) {
     log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")

examples/paramsHelp/pipeline/nextflow.config

@@ -1,5 +1,5 @@
 plugins {
-  id 'nf-validation@2.0.0'
+  id 'nf-schema@2.0.0'
 }
 
 params {