update docs with the changes

CHANGELOG.md

@@ -2,20 +2,20 @@
 
 # Version 2.0.0 - Kagoshima
 
-:warning: This version contains a number of breaking changes. Please read the changelog carefully before upgrading. :warning:
-
-To migrate your schemas please follow the [migration guide](https://nextflow-io.github.io/nf-validation/latest/migration_guide/)
+To migrate from nf-validation please follow the [migration guide](https://nextflow-io.github.io/nf-validation/latest/migration_guide/)
 
 ## New features
 
 - Added the `uniqueEntries` keyword. This keyword takes a list of strings corresponding to names of fields that need to be a unique combination. e.g. `uniqueEntries: ['sample', 'replicate']` will make sure that the combination of the `sample` and `replicate` fields is unique. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
+- Added `samplesheetToList` which is the function equivalent of `.fromSamplesheet` [#3](https://github.com/nextflow-io/nf-schema/pull/3)
 
 ## Changes
 
 - Changed the used draft for the schema from `draft-07` to `draft-2020-12`. See the [2019-09](https://json-schema.org/draft/2019-09/release-notes) and [2020-12](https://json-schema.org/draft/2020-12/release-notes) release notes for all changes ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - Removed all validation code from the `.fromSamplesheet()` channel factory. The validation is now solely done in the `validateParameters()` function. A custom error message will now be displayed if any error has been encountered during the conversion ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - Removed the `unique` keyword from the samplesheet schema. You should now use [`uniqueItems`](https://json-schema.org/understanding-json-schema/reference/array#uniqueItems) or `uniqueEntries` instead ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - Removed the `skip_duplicate_check` option from the `fromSamplesheet()` channel factory and the `--validationSkipDuplicateCheck` parameter. You should now use the `uniqueEntries` or [`uniqueItems`](https://json-schema.org/understanding-json-schema/reference/array#uniqueItems) keywords in the schema instead ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
+- `.fromSamplesheet()` now is a channel operator instead of a channel factory. It takes one required argument which can either be a string containing the relative path to the schema or a file object of the schema [#3](https://github.com/nextflow-io/nf-schema/pull/3)
 - `.fromSamplesheet()` now does dynamic typecasting instead of using the `type` fields in the JSON schema. This is done due to the complexity of `draft-2020-12` JSON schemas. This should not have that much impact but keep in mind that some types can be different between this and earlier versions because of this ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - `.fromSamplesheet()` will now set all missing values as `[]` instead of the type specific defaults (because of the changes in the previous point). This should not change that much as this will also result in `false` when used in conditions. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 
@@ -25,133 +25,3 @@ To migrate your schemas please follow the [migration guide](https://nextflow-io.
 - The `schema` keyword will now work in all schemas. ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - Improved the error messages ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
 - `.fromSamplesheet()` now supports deeply nested samplesheets ([#141](https://github.com/nextflow-io/nf-validation/pull/141))
-
-# Version 1.1.3 - Asahikawa
-
-## Improvements
-
-- Added support for double quotes (`"`) in CSV and TSV samplesheets ([#134](https://github.com/nextflow-io/nf-validation/pull/134))
-
-# Version 1.1.2 - Wakayama
-
-## Bug fixes
-
-- Fixed an issue with inputs using `file-path-pattern` where only one file was found (`Path` casting to `ArrayList` error) ([#132](https://github.com/nextflow-io/nf-validation/pull/132))
-
-# Version 1.1.1 - Shoyu
-
-## Bug fixes
-
-- Fixed an issue where samplesheet with a lot of null values would take forever to validate ([#120](https://github.com/nextflow-io/nf-validation/pull/120)) => Thanks @awgymer for fixing this!
-- Now YAML files are actually validated instead of skipped ([#124](https://github.com/nextflow-io/nf-validation/pull/120))
-
-# Version 1.1.0 - Miso
-
-## Features
-
-- Add support for samplesheets with no header ([#115](https://github.com/nextflow-io/nf-validation/pull/115))
-
-## Bug fixes
-
-- Floats and doubles should now be created when using the `number` type in the schema ([#113](https://github.com/nextflow-io/nf-validation/pull/113/))
-- When `0` is used as a default value in the schema, a `0` will now be used as the value in the `.fromSamplesheet()` channel instead of `null` ([#114](https://github.com/nextflow-io/nf-validation/pull/114))
-
-## New features
-
-- Added `file-path-pattern` format to check every file fetched using a glob pattern. Using a glob is now also possible in the samplesheet and will create a list of all files found using that glob pattern. ([#118](https://github.com/nextflow-io/nf-validation/pull/118))
-
-# Version 1.0.0 - Tonkotsu
-
-The nf-validation plugin is now in production use across many pipelines and has (we hope) now reached a point of relative stability. The bump to major version v1.0.0 signifies that it is suitable for use in production pipelines.
-
-This version also introduces a small breaking change of syntax when providing optional arguments to the functions. You can now provide optional arguments such as the nextflow parameters schema path as:
-`validateParameters(parameters_schema: 'my_file.json')`
-
-(previous syntax used positional arguments instead).
-
-## Bug fixes
-
-- The path to a custom parameters schema must be provided through a map '`parameters_schema: 'my_file.json'`' in `validateParameters()` and `paramsSummaryMap()` ([#108](https://github.com/nextflow-io/nf-validation/pull/108))
-
-# Version 0.3.4
-
-This version introduced a bug which made all pipeline runs using the function `validateParameters()` without providing any arguments fail.
-
-This bug causes Nextflow to exit with an error on launch for most pipelines. It should not be used. It was [removed](https://github.com/nextflow-io/plugins/pull/40) from the Nextflow Plugin registry to avoid breaking people's runs.
-
-### Bug fixes
-
-- Do not check S3 URL paths with `PathValidator` `FilePathValidator` and `DirectoryPathValidator` ([#106](https://github.com/nextflow-io/nf-validation/pull/106))
-- Make monochrome_logs an option in `paramsSummaryLog()`, `paramsSummaryMap()` and `paramsHelp()` instead of a global parameter ([#101](https://github.com/nextflow-io/nf-validation/pull/101))
-
-# Version 0.3.3
-
-### Bug fixes
-
-- Do not check if S3 URL paths exists to avoid AWS errors, and add a new parameter `validationS3PathCheck` ([#104](https://github.com/nextflow-io/nf-validation/pull/104))
-
-# Version 0.3.2
-
-### Bug fixes
-
-- Add parameters defined on the top level of the schema and within the definitions section as expected params ([#79](https://github.com/nextflow-io/nf-validation/pull/79))
-- Fix error when a parameter is not present in the schema and evaluates to false ([#89](https://github.com/nextflow-io/nf-validation/pull/89))
-- Changed the `schema_filename` option of `fromSamplesheet` to `parameters_schema` to make this option more clear to the user ([#91](https://github.com/nextflow-io/nf-validation/pull/91))
-
-## Version 0.3.1
-
-### Bug fixes
-
-- Don't check if path exists if param is not true ([#74](https://github.com/nextflow-io/nf-validation/pull/74))
-- Don't validate a file if the parameter evaluates to false ([#75](https://github.com/nextflow-io/nf-validation/pull/75))
-
-## Version 0.3.0
-
-### New features
-
-- Check that a sample sheet doesn't have duplicated entries by default. Can be disabled with `--validationSkipDuplicateCheck` ([#72](https://github.com/nextflow-io/nf-validation/pull/72))
-
-### Bug fixes
-
-- Only validate a path if it is not null ([#50](https://github.com/nextflow-io/nf-validation/pull/50))
-- Only validate a file with a schema if the file path is provided ([#51](https://github.com/nextflow-io/nf-validation/pull/51))
-- Handle errors when sample sheet not provided or doesn't have a schema ([#56](https://github.com/nextflow-io/nf-validation/pull/56))
-- Silently ignore samplesheet fields that are not defined in samplesheet schema ([#59](https://github.com/nextflow-io/nf-validation/pull/59))
-- Correctly handle double-quoted fields containing commas in csv files by `.fromSamplesheet()` ([#63](https://github.com/nextflow-io/nf-validation/pull/63))
-- Print param name when path does not exist ([#65](https://github.com/nextflow-io/nf-validation/pull/65))
-- Fix file or directory does not exist error not printed when it was the only error in a samplesheet ([#65](https://github.com/nextflow-io/nf-validation/pull/65))
-- Do not return parameter in summary if it has no default in the schema and is set to 'false' ([#66](https://github.com/nextflow-io/nf-validation/pull/66))
-- Skip the validation of a file if the path is an empty string and improve error message when the path is invalid ([#69](https://github.com/nextflow-io/nf-validation/pull/69))
-
-### Deprecated
-
-- The meta map of input channels is not an ImmutableMap anymore ([#68](https://github.com/nextflow-io/nf-validation/pull/68)). Reason: [Issue #52](https://github.com/nextflow-io/nf-validation/issues/52)
-
-## Version 0.2.1
-
-### Bug fixes
-
-- Fixed a bug where `immutable_meta` option in `fromSamplesheet()` wasn't working when using `validateParameters()` first. (@nvnieuwk)
-
-## Version 0.2.0
-
-### New features
-
-- Added a new [documentation site](https://nextflow-io.github.io/nf-validation/). (@ewels and @mashehu)
-- Removed the `file-path-exists`, `directory-path-exists` and `path-exists` and added a [`exists`](https://nextflow-io.github.io/nf-validation/nextflow_schema/nextflow_schema_specification/#exists) parameter to the schema. (@mirpedrol)
-- New [`errorMessage`](https://nextflow-io.github.io/nf-validation/nextflow_schema/nextflow_schema_specification/#errormessage) parameter for the schema which can be used to create custom error messages. (@mirpedrol)
-- Samplesheet validation now happens in `validateParameters()` using the schema specified by the `schema` parameter in the parameters schema. (@mirpedrol)
-
-### Improvements
-
-- The `meta` maps are now immutable by default, see [`ImmutableMap`](https://nextflow-io.github.io/nf-validation/samplesheets/immutable_map/) for more info (@nvnieuwk)
-- `validateAndConvertSamplesheet()` has been renamed to `fromSamplesheet()`
-- Refactor `--schema_ignore_params` to `--validationSchemaIgnoreParams`
-
-### Bug fixes
-
-- Fixed a bug where an empty meta map would be created when no meta values are in the samplesheet schema. (@nvnieuwk)
-
-## Version 0.1.0
-
-Initial release.

README.md

@@ -50,9 +50,8 @@ validateParameters()
 // Print summary of supplied parameters
 log.info paramsSummaryLog(workflow)
 
-// Create a new channel of metadata from a sample sheet
-// NB: `input` corresponds to `params.input` and associated sample sheet schema
-ch_input = Channel.fromSamplesheet("input")
+// Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
+ch_input = Channel.of(params.input).fromSamplesheet("assets/schema_input.json")
 ```
 
 ## Dependencies
@@ -62,7 +61,7 @@ ch_input = Channel.fromSamplesheet("input")
 
 ## Slack channel
 
-There is a dedicated [nf-validation Slack channel](https://nfcore.slack.com/archives/C056RQB10LU) in the [Nextflow Slack workspace](nextflow.slack.com).
+There is a dedicated [nf-validation Slack channel](https://nfcore.slack.com/archives/C056RQB10LU) in the [Nextflow Slack workspace](https://nextflow.slack.com).
 
 ## Credits
 

docs/background.md

@@ -15,3 +15,5 @@ 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-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.
+
+Earlier versions of the plugin can be found in the [nf-validation](https://github.com/nextflow-io/nf-validation) repository and can still be used in the pipeline. However the nf-validation plugin is no longer supported and all development has been moved to nf-schema.

docs/migration_guide.md

@@ -1,21 +1,22 @@
 ---
 title: Migration guide
-description: Guide to migrate pipelines using nf-schema pre v2.0.0 to after v2.0.0
+description: Guide to migrate pipelines from nf-validation to nf-schema
 hide:
   - toc
 ---
 
 # Migration guide
 
-This guide is intended to help you migrate your pipeline from older versions of the plugin to version 2.0.0 and later.
+This guide is intended to help you migrate your pipeline from [nf-validation](https://github.com/nextflow-io/nf-validation) to nf-schema.
 
 ## Major changes in the plugin
 
-Following list shows the major breaking changes introduced in version 2.0.0:
+Following list shows the major breaking changes introduced in nf-schema:
 
 1. The JSON schema draft has been updated from `draft-07` to `draft-2020-12`. See [JSON Schema draft 2020-12 release notes](https://json-schema.org/draft/2020-12/release-notes) and [JSON schema draft 2019-09 release notes](https://json-schema.org/draft/2019-09/release-notes) for more information.
-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
+2. The `fromSamplesheet` channel factory has been converted to a channel operator. See [updating `fromSamplesheet`](#updating-fromsamplesheet) for more information.
+3. 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.
+4. 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-schema/blob/master/CHANGELOG.md).
 
@@ -31,9 +32,27 @@ This will replace the old schema draft specification (`draft-07`) by the new one
 
 !!! note
 
-    Repeat this command for every JSON schema you use in your pipeline. e.g. for the default samplesheet schema:
+    Repeat this command for every JSON schema you use in your pipeline. e.g. for the default samplesheet schema in nf-core pipelines:
     `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' assets/schema_input.json `
 
+Next you should update the `.fromSamplesheet` channel factory to the channel operator. Following tabs shows the difference between the versions:
+
+=== "nf-validation"
+
+    ```groovy
+    Channel.fromSamplesheet("input")
+    ```
+
+=== "nf-schema"
+
+    ```groovy
+    Channel.of(params.input).fromSamplesheet("path/to/samplesheet/schema")
+    ```
+
+!!! note
+
+    This change was necessary to make it possible for pipelines to be used as pluggable workflows. This also enables the validation and conversion of files generated by the pipeline.
+
 If you are using any special features in your schemas, you will need to update your schemas manually. Please refer to the [JSON Schema draft 2020-12 release notes](https://json-schema.org/draft/2020-12/release-notes) and [JSON schema draft 2019-09 release notes](https://json-schema.org/draft/2019-09/release-notes) for more information.
 
 However here are some guides to the more common migration patterns:
@@ -44,7 +63,7 @@ When you use `unique` in your schemas, you should update it to use `uniqueItems`
 
 If you used the `unique:true` field, you should update it to use `uniqueItems` like this:
 
-=== "Before v2.0"
+=== "nf-validation"
 
     ```json hl_lines="9"
     {
@@ -62,7 +81,7 @@ If you used the `unique:true` field, you should update it to use `uniqueItems` l
     }
     ```
 
-=== "After v2.0"
+=== "nf-schema"
 
     ```json hl_lines="12"
     {
@@ -82,7 +101,7 @@ If you used the `unique:true` field, you should update it to use `uniqueItems` l
 
 If you used the `unique: ["field1", "field2"]` field, you should update it to use `uniqueEntries` like this:
 
-=== "Before v2.0"
+=== "nf-validation"
 
     ```json hl_lines="9"
     {
@@ -100,7 +119,7 @@ If you used the `unique: ["field1", "field2"]` field, you should update it to us
     }
     ```
 
-=== "After v2.0"
+=== "nf-schema"
 
     ```json hl_lines="12"
     {
@@ -122,7 +141,7 @@ If you used the `unique: ["field1", "field2"]` field, you should update it to us
 
 When you use `dependentRequired` in your schemas, you should update it like this:
 
-=== "Before v2.0"
+=== "nf-validation"
 
     ```json hl_lines="12"
     {
@@ -142,7 +161,7 @@ When you use `dependentRequired` in your schemas, you should update it like this
     }
     ```
 
-=== "After v2.0"
+=== "nf-schema"
 
     ```json hl_lines="14 15 16"
     {

docs/nextflow_schema/create_schema.md

@@ -76,4 +76,6 @@ This web interface is where you should add detail to your schema, customising th
 
     There is currently no tooling to help you write sample sheet schema :anguished:
 
+    You can find an example in [Example sample sheet schema](sample_sheet_schema_examples.md)
+
     Watch this space..