From 4d5828d26d9dc66898da013276e690f3f8f232fe Mon Sep 17 00:00:00 2001
From: Jorge Aguilera <jagedn@gmail.com>
Date: Wed, 21 Feb 2024 09:28:45 +0100
Subject: [PATCH] add asciidoctor plugin and gh-pages

Signed-off-by: Jorge Aguilera <jagedn@gmail.com>
---
 .github/workflows/ghpages.yml        | 49 +++++++++++++++++++++++
 build.gradle                         | 18 +++++++++
 gradle.properties                    |  1 +
 src/docs/asciidoc/index.adoc         |  8 ++++
 src/docs/asciidoc/parts/example.adoc | 58 ++++++++++++++++++++++++++++
 src/docs/asciidoc/parts/intro.adoc   |  3 ++
 src/docs/asciidoc/parts/setup.adoc   |  4 ++
 7 files changed, 141 insertions(+)
 create mode 100644 .github/workflows/ghpages.yml
 create mode 100644 build.gradle
 create mode 100644 gradle.properties
 create mode 100644 src/docs/asciidoc/index.adoc
 create mode 100644 src/docs/asciidoc/parts/example.adoc
 create mode 100644 src/docs/asciidoc/parts/intro.adoc
 create mode 100644 src/docs/asciidoc/parts/setup.adoc

diff --git a/.github/workflows/ghpages.yml b/.github/workflows/ghpages.yml
new file mode 100644
index 0000000..a6625b0
--- /dev/null
+++ b/.github/workflows/ghpages.yml
@@ -0,0 +1,49 @@
+name: ghpages
+on:
+  push:
+    branches:
+      - 'main'
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build docu
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    steps:
+      - name: Environment
+        run: env | sort
+      - uses: actions/checkout@v4
+      - name: Set up JDK for x64
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+          architecture: x64
+      - name: Generate
+        run: ./gradlew asciidoctor
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: ./build/docs/asciidoc
+
+  publish-ghpages:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2
\ No newline at end of file
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..6ea876a
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,18 @@
+buildscript {
+    repositories {
+        mavenCentral()
+    }
+}
+
+plugins {
+    id("org.asciidoctor.jvm.convert") version "3.3.2"
+}
+
+repositories {
+    mavenCentral()
+}
+
+asciidoctor{
+    baseDir 'src/docs/asciidoc'
+    attributes revnumber : { project.version.toString() }
+}
\ No newline at end of file
diff --git a/gradle.properties b/gradle.properties
new file mode 100644
index 0000000..8766f31
--- /dev/null
+++ b/gradle.properties
@@ -0,0 +1 @@
+version=0.0.2-rc1
\ No newline at end of file
diff --git a/src/docs/asciidoc/index.adoc b/src/docs/asciidoc/index.adoc
new file mode 100644
index 0000000..b27b291
--- /dev/null
+++ b/src/docs/asciidoc/index.adoc
@@ -0,0 +1,8 @@
+= nf-nomad
+:toc: left
+
+include::parts/intro.adoc[]
+
+include::parts/example.adoc[]
+
+include::parts/setup.adoc[]
\ No newline at end of file
diff --git a/src/docs/asciidoc/parts/example.adoc b/src/docs/asciidoc/parts/example.adoc
new file mode 100644
index 0000000..47df5d6
--- /dev/null
+++ b/src/docs/asciidoc/parts/example.adoc
@@ -0,0 +1,58 @@
+== Example
+
+.nextflow.config
+[source]
+----
+plugins {
+  id 'nf-nomad@0.0.1'
+  id 'nf-amazon'
+}
+
+fusion {
+    enabled = true
+    exportStorageCredentials=true
+}
+
+wave {
+    enabled = true
+}
+
+nomad{
+    client{
+        address = "http://localhost:4646"
+    }
+    jobs{
+        deleteOnCompletion = false
+    }
+}
+
+process.executor ='nomad'
+----
+
+.main.nf
+[source]
+----
+process sayHello {
+    container   'ubuntu:20.04'
+
+    input:
+    val x
+    output:
+    stdout
+    script:
+    """
+    echo '$x world!'
+    """
+}
+
+workflow {
+    Channel.of('Bonjour', 'Ciao', 'Hello', 'Hola') | sayHello | view
+}
+----
+
+TIP:: You need to use an S3 bucket as working dir
+
+Run the pipeline
+
+`$ nextflow run main.nf`
+
diff --git a/src/docs/asciidoc/parts/intro.adoc b/src/docs/asciidoc/parts/intro.adoc
new file mode 100644
index 0000000..2134f38
--- /dev/null
+++ b/src/docs/asciidoc/parts/intro.adoc
@@ -0,0 +1,3 @@
+== Introduction
+
+The aim of this plugin
\ No newline at end of file
diff --git a/src/docs/asciidoc/parts/setup.adoc b/src/docs/asciidoc/parts/setup.adoc
new file mode 100644
index 0000000..8fa6735
--- /dev/null
+++ b/src/docs/asciidoc/parts/setup.adoc
@@ -0,0 +1,4 @@
+== Setup
+
+Firstly you need a `nomad` cluster. See https://developer.hashicorp.com/nomad/intro
+