Merge branch 'master' into 4920_azure_tasks_support_disk_directive

nextflow-io · Dec 5, 2024 · 91de04f · 91de04f
2 parents 7172d80 + 5c5a810
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diff --git a/.github/workflows/seqeradocs-changelog.yml b/.github/workflows/seqeradocs-changelog.yml
@@ -0,0 +1,62 @@
+name: Push release change log to Seqera Docs
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      release_name:
+        description: "Release version (e.g. 1.0.0)"
+        required: true
+      release_body:
+        description: "Release changelog content"
+        required: true
+
+jobs:
+  update-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Clone seqeralabs/docs
+        run: |
+          git clone https://github.com/seqeralabs/docs.git seqeralabs-docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Create changelog file
+        run: |
+          mkdir -p seqeralabs-docs/changelog/nextflow
+          cat << EOF > seqeralabs-docs/changelog/nextflow/${{ github.event.release.name || inputs.release_name }}.mdx
+          ---
+          title: Nextflow ${{ github.event.release.name || inputs.release_name }}
+          date: $(date +%Y-%m-%d)
+          tags: [nextflow]
+          ---
+
+          ${{ github.event.release.body || inputs.release_body }}
+          EOF
+
+      - uses: actions/create-github-app-token@v1
+        id: generate-token
+        with:
+          app-id: ${{ secrets.DOCS_BOT_APP_ID }}
+          private-key: ${{ secrets.DOCS_BOT_APP_PRIVATE_KEY }}
+          owner: seqeralabs
+          repositories: docs
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          branch-token: ${{ steps.generate-token.outputs.token }}
+          path: seqeralabs-docs
+          commit-message: "Changelog: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          title: "Changelog: Nextflow ${{ github.event.release.name || inputs.release_name }}"
+          body: |
+            This PR adds the changelog for Nextflow ${{ github.event.release.name || inputs.release_name }} to the Seqera documentation.
+
+            This is an automated PR created from the Nextflow repository.
+          branch: changelog-nextflow-${{ github.event.release.name || inputs.release_name }}
+          base: master
+          delete-branch: true
diff --git a/docs/_static/dag.mmd b/docs/_static/dag.mmd
@@ -1,3 +1,17 @@
+%%{
+    init: {
+        'theme': 'base',
+        'themeVariables': {
+            'primaryColor': '#B6ECE2',
+            'primaryTextColor': '#160F26',
+            'primaryBorderColor': '#065647',
+            'lineColor': '#545555',
+            'clusterBkg': '#BABCBD22',
+            'clusterBorder': '#DDDEDE',
+            'fontFamily': 'arial'
+        }
+    }
+}%%
 flowchart TB
     subgraph " "
     v0["Channel.fromFilePairs"]

diff --git a/docs/aws.md b/docs/aws.md
@@ -539,7 +539,8 @@ See the AWS documentation for details how to create the required AWS Batch queue
 and the Batch Execution Role.
 
 :::{note}
-This feature requires the use {ref}`Wave <wave-page>` container provisioning service.
+Nextflow uses [s5cmd](https://github.com/peak/s5cmd) to download the task input data and upload the task outputs.
+To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See {ref}`Wave <wave-page>` documentation for more details.
 :::
 
 ## Advanced configuration

diff --git a/docs/azure.md b/docs/azure.md
@@ -155,7 +155,7 @@ Replacing `<PIPELINE NAME>` with a pipeline name e.g. `nextflow-io/rnaseq-nf` an
 
 See the [Batch documentation](https://docs.microsoft.com/en-us/azure/batch/quick-create-portal) for further details about the configuration for Azure Batch.
 
-### Pools configuration
+### Autopools
 
 When using the `autoPoolMode` option, Nextflow automatically creates a `pool` of compute nodes appropriate for your pipeline.
 

diff --git a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
@@ -19,6 +19,20 @@
 </head>
 <body>
 <pre class="mermaid" style="text-align: center;">
+%%{
+  init: {
+    'theme': 'base',
+    'themeVariables': {
+      'primaryColor': '#B6ECE2',
+      'primaryTextColor': '#160F26',
+      'primaryBorderColor': '#065647',
+      'lineColor': '#545555',
+      'clusterBkg': '#BABCBD22',
+      'clusterBorder': '#DDDEDE',
+      'fontFamily': 'arial'
+    }
+  }
+}%%
 REPLACE_WITH_NETWORK_DATA
 </pre>
 <script type="module">