Merge pull request #29 from CCBR/docs

Create documentation website

.gitattributes

@@ -4,3 +4,4 @@ modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
 *.config linguist-language=nextflow
 assets/** linguist-generated
+_extensions/** linguist-generated

.github/CONTRIBUTING.md

@@ -30,7 +30,7 @@ Pre-commit will run the hooks every time you commit.
 
 Keep the changelog up to date with all notable changes in `CHANGELOG.md`[^2].
 
-[^2]: changelog guidelines: https://keepachangelog.com/en/1.1.0/
+[^2]: changelog guidelines: <https://keepachangelog.com/en/1.1.0/>
 
 ## VS code extensions
 

.github/workflows/quarto-publish.yml

@@ -0,0 +1,50 @@
+name: Render and Publish
+
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+    paths:
+      - "**.md"
+      - "**.qmd"
+      - "**.yml"
+
+permissions:
+  contents: write
+  pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v3
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install Python packages
+        run: |
+          pip install --upgrade pip -r docs/requirements.txt
+
+      - name: Install R packages
+        shell: Rscript {0}
+        run: |
+          install.packages(c('dplyr', 'glue', 'here', 'knitr', 'tidyr'. 'yaml'))
+
+      - name: prerender
+        run: |
+          python docs/create-listings.py
+
+      - name: Publish to GitHub Pages (and render)
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -14,3 +14,11 @@ test.tap
 test_output/
 tests/data/
 work/
+
+/docs/modules/
+/docs/subworkflows/
+/_freeze/
+/_site/
+/.quarto/
+.Rproj.user
+*.Rproj

.pre-commit-config.yaml

@@ -1,6 +1,11 @@
 default_install_hook_types: [pre-commit, commit-msg]
 default_stages: [pre-commit]
-exclude: ^assets/
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3

.prettierignore

@@ -6,3 +6,4 @@ results/
 .DS_Store
 *.code-workspace
 assets/*.html
+_extensions

CHANGELOG.md

@@ -1,5 +1,7 @@
 ## Development version
 
+Our documentation website is now live: <https://ccbr.github.io/nf-modules/> (#16)
+
 ### New modules
 
 - bwa/index

README.md

@@ -3,6 +3,7 @@
 Reusable modules and subworkflows for Nextflow pipelines
 
 [![test](https://github.com/CCBR/nf-modules/actions/workflows/test.yml/badge.svg)](https://github.com/CCBR/nf-modules/actions/workflows/test.yml)
+[![docs](https://img.shields.io/badge/docs-📖-blue)](https://ccbr.github.io/nf-modules/)
 
 ## Usage
 
@@ -38,7 +39,7 @@ Come across a **bug**? Open an [issue](https://github.com/CCBR/nf-modules/issues
 
 Have a **question**? Ask it in [discussions](https://github.com/CCBR/nf-modules/discussions).
 
-Want to **contribute** to this project? Check out the [contributing guidelines](.github/CONTRIBUTING.md).
+Want to **contribute** to this project? Check out the [contributing guidelines](/.github/CONTRIBUTING.md).
 
 ## References