diff --git a/.github/workflows/seqeradocs-changelog.yml b/.github/workflows/seqeradocs-changelog.yml new file mode 100644 index 0000000000..f41058fe71 --- /dev/null +++ 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 index 0963e2c106..989a536ae9 100644 --- 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 index ba518ad7ae..3de628e3cc 100644 --- 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 ` 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 ` documentation for more details. ::: ## Advanced configuration diff --git a/docs/azure.md b/docs/azure.md index 61269e43ac..57787bd5bf 100644 --- a/docs/azure.md +++ b/docs/azure.md @@ -155,7 +155,7 @@ Replacing `` 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 index 47062c1218..0ab1d9475e 100644 --- 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 @@
+%%{
+  init: {
+    'theme': 'base',
+    'themeVariables': {
+      'primaryColor': '#B6ECE2',
+      'primaryTextColor': '#160F26',
+      'primaryBorderColor': '#065647',
+      'lineColor': '#545555',
+      'clusterBkg': '#BABCBD22',
+      'clusterBorder': '#DDDEDE',
+      'fontFamily': 'arial'
+    }
+  }
+}%%
 REPLACE_WITH_NETWORK_DATA