Bump Nextflow Versions (#7019)

* ci(renovate): Add custom VERSION updates in GitHub actions https://docs.renovatebot.com/presets-customManagers/#custommanagersgithubactionsversions * ci(#6664): Bump all Nextflow versions to 24.10.1 * ci: Add renovate comments to version in actions
nf-core · Nov 19, 2024 · c0ef8c3 · c0ef8c3
1 parent 3a89745
commit c0ef8c3
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Showing 9 changed files with 48 additions and 16 deletions.
diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -24,6 +24,8 @@ runs:
 
     - name: Setup Nextflow
       uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
       uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
@@ -33,7 +35,7 @@ runs:
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
       with:
-        version: "0.9.2"
+        version: "${{ env.NFTEST_VERSION }}"
         install-pdiff: true
 
     - name: Setup apptainer

diff --git a/.github/renovate.json5 b/.github/renovate.json5
@@ -7,8 +7,24 @@
     "prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
     "packageRules": [
         {
-            "matchDatasources": ["conda", "pypi", "docker"],
+            "matchDatasources": [
+                "conda",
+                "pypi",
+                "docker"
+            ],
             "automerge": false
         }
-    ]
+    ],
+        "customManagers": [
+            {
+                "customType": "regex",
+                "fileMatch": [
+                    "(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$",
+                    "(^|/)action\\.ya?ml$"
+                ],
+                "matchStrings": [
+                    "# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
+                ]
+            }
+        ]
 }
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
@@ -29,11 +29,13 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.2"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-  NXF_VER: "24.04.4"
+  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
 
 jobs:
   nf-test-gpu:

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -28,6 +28,8 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VER: "24.10.1"
 
 jobs:
   pre-commit:

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -26,11 +26,13 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.2"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-  NXF_VER: "24.04.4"
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
 
 jobs:
   nf-test:

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
@@ -28,6 +28,8 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
 
 jobs:
   pytest-changes:
@@ -263,6 +265,8 @@ jobs:
 
       - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ env.NXF_VERSION }}
 
       - name: Setup apptainer
         if: matrix.profile == 'singularity'

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
@@ -10,8 +10,12 @@ on:
 # TODO Skip testing CI if any changes to environment.yml
 
 env:
-  WAVE_VER: "1.5.0"
-  NFTEST_VER: "0.9.1"
+  # renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
+  WAVE_VERSION: "1.5.0"
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.1"
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
 
 jobs:
   generate-matrix:
@@ -62,8 +66,8 @@ jobs:
 
       - name: Install wave-cli
         run: |
-          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
-          sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
+          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
+          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
           chmod +x /usr/local/bin/wave
 
       - name: Build ${{ matrix.profile }} container
@@ -98,8 +102,8 @@ jobs:
 
       - name: Install wave-cli
         run: |
-          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
-          sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
+          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
+          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
           chmod +x /usr/local/bin/wave
 
       - name: Create a registry name
@@ -139,7 +143,7 @@ jobs:
 
   #     - uses: nf-core/setup-nf-test@v1
   #       with:
-  #         version: ${{ env.NFTEST_VER }}
+  #         version: ${{ env.NFTEST_VERSION }}
 
   #     - name: Bump Snapshot Versions
   #       env:

diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
@@ -43,5 +43,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.10.1'
 }
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
@@ -56,5 +56,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.10.1'
 }