Merge branch 'dev' into precommit_largefiles

Author: mashehu

.devcontainer/build-devcontainer/Dockerfile

@@ -1,6 +1,6 @@
 # devcontainers/miniconda image based on debian (bookworm)
 # see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
-FROM mcr.microsoft.com/devcontainers/miniconda@sha256:b99720fe7bdce0346dc3c3ff54414ba78ff183d85a5a9d9a2e2e5775ce679347 AS build
+FROM mcr.microsoft.com/devcontainers/miniconda@sha256:68c1f6d7904f2d94ce54a43052155348bdcf1800d9f84e8b7fd367c85e688bf1 AS build
 
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
@@ -27,7 +27,7 @@ RUN rm -f /etc/apt/sources.list.d/yarn.list && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM mcr.microsoft.com/devcontainers/base:2.1.6-debian12@sha256:15143a8c806afb8db57ae2c92876c112d7a6a1ced31cd7aa8b414201782757a4 AS final
+FROM mcr.microsoft.com/devcontainers/base:2.1.8-debian12@sha256:17e6cc517b483d1108b333d4c34352b0a21617f0117052e9b259d47113a9dc37 AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda

.devcontainer/setup.sh

@@ -10,7 +10,7 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 nextflow self-update
 
 # Install specifically the version of tools from the workspace
-uv sync --all-extras
+uv sync
 
 # Activate the virtual environment automatically on login
 echo "source $(pwd)/.venv/bin/activate" >> $HOME/.bashrc

.gitattributes

@@ -0,0 +1 @@
+CHANGELOG.md merge=union

.github/actions/create-lint-wf/action.yml

@@ -16,7 +16,7 @@ runs:
         export NXF_WORK=$(pwd)
 
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: ${{ matrix.NXF_VER }}
 
@@ -40,34 +40,46 @@ runs:
         pwd
         ls -l
       working-directory: create-lint-wf/nf-core-testpipeline
+
     # Run code style linting
-    - name: run pre-commit
+    - name: run prek
       shell: bash
-      run: uv run pre-commit run --all-files
-      working-directory: create-lint-wf
+      run: uv run prek run --config .pre-commit-config.yaml --all-files
+      working-directory: create-lint-wf/nf-core-testpipeline
 
     # Update modules to the latest version
     - name: nf-core modules update
       shell: bash
       run: uv run nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
       working-directory: create-lint-wf
 
+    # Commit regenerated container configs so lint sees them as up to date
+    - name: commit updated container configs
+      shell: bash
+      run: |
+        cd nf-core-testpipeline
+        git config user.email "nf-core-bot@nf-co.re"
+        git config user.name "nf-core-bot"
+        git add conf/containers_*.config
+        git diff --cached --quiet || git commit -m "Update container configs after modules update"
+      working-directory: create-lint-wf
+
     # Remove TODO statements
     - name: remove TODO
       shell: bash
-      run: find nf-core-testpipeline -type f -exec sed -i 's#TODO nf-core:##g' {} \;
+      run: find nf-core-testpipeline -not -path '*/.git/*' -type f -exec sed -i 's#TODO nf-core:##g' {} \;
       working-directory: create-lint-wf
 
     # Uncomment includeConfig statement
     - name: uncomment include config
       shell: bash
-      run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
+      run: find nf-core-testpipeline -not -path '*/.git/*' -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \;
       working-directory: create-lint-wf
 
     # Replace zenodo.XXXXXX to pass readme linting
     - name: replace zenodo.XXXXXX
       shell: bash
-      run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+      run: find nf-core-testpipeline -not -path '*/.git/*' -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
     # Run nf-core pipelines linting
@@ -88,7 +100,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
+      uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/snapshots/gpu.nf.test.snap

@@ -107,7 +107,7 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.0"
+            "nextflow": "25.10.4"
         },
         "timestamp": "2025-06-16T14:29:10.076573"
     }

.github/workflows/branch.yml

@@ -18,7 +18,7 @@ jobs:
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@ffd016c7e151d97d69d21a843022fd4cd5b96fe5 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         with:
           message: |
             ## This PR is against the `main` branch :x:

.github/workflows/changelog.py

@@ -135,9 +135,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
     # If the line already contains a link to the PR, don't add it again.
     line = _skip_existing_entry_for_this_pr(line, same_section=False)
 
-    if (
-        line.startswith("## ") and not line.strip() == "# nf-core/tools: Changelog"
-    ):  # Version header, e.g. "## v2.12dev"
+    if line.startswith("## ") and line.strip() != "# nf-core/tools: Changelog":  # Version header, e.g. "## v2.12dev"
         print(f"Found version header: {line.strip()}")
         updated_lines.append(line)
 

.github/workflows/changelog.yml

@@ -2,26 +2,23 @@ name: Update CHANGELOG.md
 on:
   issue_comment:
     types: [created] # Add "@nf-core-bot changelog" as a PR comment to trigger this workflow.
-  pull_request_target:
-    types: [opened]
-    branches:
-      - dev
 
 jobs:
   update_changelog:
     runs-on: ubuntu-latest
+    if: contains(github.event.comment.body, '@nf-core-bot changelog')
 
     steps:
       - name: branch-deploy
         id: branch-deploy
         if: github.event_name == 'issue_comment'
-        uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2
+        uses: github/branch-deploy@de4d10ee17c3117a2076aff489ba03fadf225f35 # v11.1.5
         with:
           trigger: "@nf-core-bot changelog"
           reaction: "eyes"
           stable_branch: "dev"
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -31,14 +28,10 @@ jobs:
         env:
           GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
         run: |
-          if [[ "${{ github.event_name }}" == "issue_comment" ]]; then
-            PR_NUMBER="${{ github.event.issue.number }}"
-          elif [[ "${{ github.event_name }}" == "pull_request_target" ]]; then
-            PR_NUMBER="${{ github.event.pull_request.number }}"
-          fi
+          PR_NUMBER="${{ github.event.issue.number }}"
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
@@ -67,12 +60,12 @@ jobs:
           echo "changed=$file_changed" >> $GITHUB_OUTPUT
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@53276d8b0d10f8b6672aa85b4588c6921d0370cc # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         continue-on-error: true
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
@@ -86,5 +79,5 @@ jobs:
           git config user.name "nf-core-bot"
           git add ${GITHUB_WORKSPACE}/CHANGELOG.md
           git status
-          git commit -m "[automated] Update CHANGELOG.md"
+          git commit -m "[automated] Update CHANGELOG.md [skip ci]"
           git push

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@1e223db275d687790206a7acac4d1a11bd6fe629 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/codspeed.yml

@@ -0,0 +1,62 @@
+name: CodSpeed benchmarks
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+
+# Cancel if a newer run with the same workflow name is queued
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  id-token: write # for OpenID Connect authentication with CodSpeed
+
+jobs:
+  startup-benchmarks:
+    name: Run start-up benchmarks
+    runs-on: codspeed-macro
+    steps:
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+        name: Check out source-code repository
+
+      - name: Set up Python
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
+        with:
+          python-version: "3.14"
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        with:
+          version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      # Clone nf-core/modules into the local cache here, while network is
+      # available. The modules-install benchmark then runs entirely offline
+      # (no per-round fetch), so it stays deterministic even if the CodSpeed
+      # step sandboxes network during measurement.
+      - name: Warm nf-core/modules cache
+        run: uv run python -c "from nf_core.modules.modules_repo import ModulesRepo; ModulesRepo()"
+
+      # These benchmarks spawn a fresh interpreter per round to measure
+      # import/start-up cost, which CodSpeed's instruction-counting
+      # "simulation" instrument can't see. Use "walltime" mode instead.
+      - name: Run start-up benchmarks
+        uses: CodSpeedHQ/action@f99becdce5e5d51fd556489ebef684f4ecfd6286 # v4.18.5
+        with:
+          mode: walltime
+          run: uv run pytest benchmarks/test_startup_benchmarks.py --codspeed