Docs marathon: Stopping for lunch

.github/workflows/pre-commit.yml

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+name: Lint code
+on:
+  push:
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/[email protected]

.pre-commit-config.yaml

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+# Config for pre-commit: https://pre-commit.com/
+---
+minimum_pre_commit_version: "2.9.2"
+repos:
+  - repo: meta
+    hooks:
+      - id: identity
+      - id: check-hooks-apply
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

.prettierignore

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+# Ignore everything
+/*
+
+# Except docs and markdown files
+!docs/
+!*.md
+!*.yml

.prettierrc

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+{
+  "tabWidth": 2,
+  "useTabs": false
+}

README.md

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-# nf-validation 
+# ![nf-validation](docs/images/nf-validation.svg)
 
-This Nextlow plugins implements a validation of pipeline parameters
-based on [nf-core JSON schema](https://nf-co.re/pipeline_schema_builder).
+## 📚 Docs 👉🏻 <https://nextflow-io.github.io/nf-validation>
 
-It can also validate and convert a samplesheet to a Nextflow channel ready to use. Supported samplesheet formats are CSV, TSV and YAML (simple).
+**A Nextflow plugin to work with validation of pipeline parameters and sample sheets.**
 
-See the [docs](https://nextflow-io.github.io/nf-validation/) for more information.
+## Introduction
+
+This plugin provides a number of functions that can be included into a Nextflow pipeline script to work with parameter and sample sheet schema. Using these functions you can:
+
+* 📖 Print usage instructions to the terminal (for use with `--help`)
+* ✍️ Print log output showing parameters with non-default values
+* ✅ Validate supplied parameters against the pipeline schema
+* 📋 Validate the contents of supplied sample sheet files
+* 🛠️ Create a Nextflow channel with a parsed sample sheet
+
+Supported sample sheet formats are CSV, TSV and YAML (simple).
+
+## Quick Start
+
+Declare the plugin in your Nextflow pipeline configuration file:
+_(make sure you pin the latest stable release version after the `@`)_
+
+```groovy title="nextflow.config"
+plugins {
+  id '[email protected]'
+}
+```
+
+This is all that is needed - Nextflow will automatically fetch the plugin code at run time.
+
+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'
+
+// Print help message, supply typical command line usage for the pipeline
+if (params.help) {
+   log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
+   exit 0
+}
+
+// Validate input parameters
+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
+// See docs for details: https://nextflow-io.github.io/nf-validation/usage/samplesheet_docs/
+ch_input = Channel.fromSamplesheet("input")
+```
+
+You can find more information on plugins in the [Nextflow documentation](https://www.nextflow.io/docs/latest/plugins.html#plugins).
+
+## Background
+
+The [Nextflow](https://nextflow.io/) workflow manager is a powerful tool for scientific workflows.
+In order for end users to launch a given workflow with different input data and varying settings, pipelines are developed using a special variable type called parameters (`params`). Defaults are hardcoded into scripts and config files but can be overwritten by user config files and command-line flags (see the [Nextflow docs](https://nextflow.io/docs/latest/config.html)).
+
+In addition to config params, a common best-practice for pipelines is to use a "sample sheet" file containing required input information. For example: a sample identifier, filenames and other sample-level metadata.
+
+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.
+
+## Dependencies
+
+- Java 11 or later
+- <https://github.com/everit-org/json-schema>
+
+## Credits
+
+This plugin was written based on code initially written within the nf-core community,
+as part of the nf-core pipeline template.
+
+We would like to thank the key contributors who include (but are not limited to):
+
+* Júlia Mir Pedrol ([@mirpedrol](https://github.com/mirpedrol))
+* Nicolas Vannieuwkerke ([@nvnieuwk](https://github.com/nvnieuwk))
+* Kevin Menden ([@KevinMenden](https://github.com/KevinMenden))
+* Phil Ewels ([@ewels](https://github.com/ewels))