Merge pull request #146 from CCBR/mkdocs-mike

set up mkdocs mike & release actions

.github/workflows/docs-mkdocs.yml

@@ -0,0 +1,25 @@
+name: docs
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "**.md"
+      - .github/workflows/docs-mkdocs.yml
+      - mkdocs.yml
+
+jobs:
+  mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}

.github/workflows/draft-release.yml

@@ -0,0 +1,25 @@
+name: draft-release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version-tag:
+        description: |
+          Semantic version tag for next release.
+          If not provided, it will be determined based on conventional commit history.
+          Example: v2.5.11
+        required: false
+        type: string
+        default: ""
+
+jobs:
+  draft-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # required to include tags
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}
+          version-tag: ${{ github.event.inputs.version-tag }}

.github/workflows/post-release.yml

@@ -0,0 +1,17 @@
+name: post-release
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}

CHANGELOG.md

@@ -25,6 +25,7 @@
 ### Misc
 
 - The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool)
+- Minor documentation updates. (#146, @kelly-sovacool)
 
 ## CARLISLE v2.5.0
 

README.md

@@ -12,6 +12,6 @@
 
 This snakemake pipeline is built to run on [Biowulf](https://hpc.nih.gov/).
 
-For comments/suggestions/advice please reach out to [Samantha Chill](mailto:samantha.sevilla@nih.gov).
+For comments/suggestions/advice please contact <mailto:CCBR_Pipeliner@mail.nih.gov>.
 
-For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) page.
+For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) website.

docs/index.md

@@ -1,3 +1,9 @@
+<!-- the README is inserted here automatically-->
+
+--8<-- "README.md"
+
+<!--- write additional info that you only want to appear in the docs index here -->
+
 The CARLISLE pipeline was developed in support of NIH [Dr Vassiliki Saloura's Laboratory](https://ccr.cancer.gov/staff-directory/vassiliki-saloura) and [Dr Javed Khan's Laboratory](https://ccr.cancer.gov/staff-directory/javed-khan/lab). It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
 
-![Image title](https://github.com/CCBR/CARLISLE/blob/dev/resources/img/CUTandRUN_Workflow.jpeg?raw=true)
+![cut-and-run workflow](img/CUTandRUN_Workflow.jpeg)

mkdocs.yml

@@ -91,7 +91,7 @@ markdown_extensions:
 
 # Page Tree
 nav:
-  - Background: index.md
+  - Home: index.md
   - Usage:
       - 1. Getting Started: user-guide/getting-started.md
       - 2. Preparing Files: user-guide/preparing-files.md