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rebrand nf-validation to nf-schema #1

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Apr 11, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/build-docs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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/src/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}}"
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2 changes: 1 addition & 1 deletion .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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/**
2 changes: 1 addition & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# nextflow-io/nf-validation: Changelog
# nextflow-io/nf-schema: Changelog

# Version 2.0.0 - Kagoshima

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10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# ![nf-validation](docs/images/nf-validation.svg)
# ![nf-schema](docs/images/nf-schema.png)

## 📚 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.**

Expand All @@ -22,7 +22,7 @@ Declare the plugin in your Nextflow pipeline configuration file:

```groovy title="nextflow.config"
plugins {
id 'nf-validation'
id 'nf-schema'
}
```

Expand All @@ -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`

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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) {
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4 changes: 2 additions & 2 deletions docs/background.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
---
title: Background
description: Get up and running with nf-validation
description: Get up and running with nf-schema
hide:
- toc
---
Expand All @@ -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.
6 changes: 3 additions & 3 deletions docs/contributing/setup.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
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83 changes: 83 additions & 0 deletions docs/images/nf-schema.svg
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The font looks off here (looks like a serif font of some form) but not sure if just a github display issue?

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Yeah I'm not sure what's going on there... The png looks fine though. @mirpedrol any ideas?

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