Merge branch 'dev' into renovate/python-3.14-slim

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@sha256:8e262a2664fab1d53054738d3633338558a2078ce66d3abde55c130f0d5da94f AS build
+FROM mcr.microsoft.com/devcontainers/miniconda@sha256:8a29f1c63ce3e138b9731f21a02a5f9aaf19454caebb670769e6fe88a573a4cb AS build
 
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
@@ -26,7 +26,7 @@ RUN apt-get update --quiet && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM mcr.microsoft.com/devcontainers/base:2.0.2-debian12@sha256:23fa69fed758b7927c60061317d73baf7d66b9fca5c344e80bce3a940b229af0 AS final
+FROM mcr.microsoft.com/devcontainers/base:2.1.5-debian12@sha256:210b178bdf27aa3cab843ff98267da72ae27fa1d8e06c415efa756048a4a1a5b AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda

.devcontainer/build-devcontainer/devcontainer.json

@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore-devcontainer-build",
 
     // installs python3.14, nf-core tools from current workspace, nextflow, nf-test,

.devcontainer/devcontainer.json

@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
     "image": "nfcore/devcontainer:dev",
 

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

@@ -88,7 +88,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/workflows/changelog.yml

@@ -19,7 +19,7 @@ jobs:
       )
 
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
@@ -65,12 +65,12 @@ jobs:
           echo "changed=$file_changed" >> $GITHUB_OUTPUT
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1
+        uses: j178/prek-action@564dda4cfa5e96aafdc4a5696c4bf7b46baae5ac # v1
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
 

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@997185467fa4f803885201cee163a9f38240193d # 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/create-lint-wf.yml

@@ -42,17 +42,17 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7
         with:
           enable-cache: true
 

.github/workflows/create-test-lint-wf-template.yml

@@ -32,7 +32,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -56,15 +56,15 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7
         with:
           enable-cache: true
 
@@ -200,7 +200,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

.github/workflows/create-test-wf.yml

@@ -41,16 +41,16 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7
         with:
           enable-cache: true
 
@@ -93,7 +93,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

.github/workflows/deploy-pypi.yml

@@ -13,16 +13,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7
         with:
           enable-cache: true