chore: Merge branch 'main' into use-tools

.github/CONTRIBUTING.md

@@ -17,7 +17,7 @@ as our collaboration process.
 Follow the steps below for detailed instructions on contributing changes to
 TOOL_NAME.
 
-![GitHub Flow diagram](./img/GitHub-Flow_bg-white.png)
+![GitHub Flow diagram](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/GitHub-Flow_bg-white.png)
 
 ### Clone the repo
 
@@ -196,9 +196,7 @@ git push --set-upstream origin iss-10
 > remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
 > remote: https://github.com/CCBR/TOOL_NAME/pull/new/iss-10 <br>
 > remote: <br>
-> To https://github.com/CCBR/TOOL_NAME <br>
-> <br>
-> [new branch] iss-10 -> iss-10 <br>
+> To https://github.com/CCBR/TOOL_NAME <br> > <br> > [new branch] iss-10 -> iss-10 <br>
 > branch 'iss-10' set up to track 'origin/iss-10'. <br>
 
 We recommend pushing your commits often so they will be backed up on GitHub.
@@ -213,7 +211,7 @@ Once your branch is ready, create a PR on GitHub:
 
 Select the branch you just pushed:
 
-![Create a new PR from your branch](./img/new-PR.png)
+![Create a new PR from your branch](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/new-PR.png)
 
 Edit the PR title and description.
 The title should briefly describe the change.
@@ -223,7 +221,7 @@ Be sure to fill out the checklist, checking off items as you complete them or
 striking through any irrelevant items.
 When you're ready, click 'Create pull request' to open it.
 
-![Open the PR after editing the title and description](./img/create-PR.png)
+![Open the PR after editing the title and description](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/create-PR.png)
 
 Optionally, you can mark the PR as a draft if you're not yet ready for it to
 be reviewed, then change it later when you're ready.

.github/workflows/build-nextflow.yml

@@ -10,15 +10,6 @@ on:
     branches:
       - main
       - develop
-  workflow_dispatch:
-    inputs:
-      test_run:
-        type: boolean
-        default: false
-        required: true
-
-env:
-  test_run: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.test_run }}
 
 jobs:
   build:
@@ -52,13 +43,6 @@ jobs:
           tool_name init
           tool_name run -c conf/ci_stub.config -stub
           popd
-      - name: Test run
-        if: ${{ env.test_run == 'true' }}
-        run: |
-          mkdir -p tmp && pushd tmp
-          tool_name init
-          tool_name run -c conf/ci_stub.config -profile docker
-          popd
       - name: "Upload Artifact"
         uses: actions/upload-artifact@v3
         if: always() # run even if previous steps fail

.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 }}

mkdocs.yml

@@ -39,6 +39,10 @@ plugins:
   - git-revision-date
   - minify:
       minify_html: true
+  - mike:
+      alias_type: symlink
+      canonical_version: latest
+      version_selector: true
 
 # Customization
 extra: