Release 3.10.0

.devcontainer/devcontainer.json

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

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/docs/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

.github/actions/get-shards/action.yml

@@ -10,6 +10,10 @@ inputs:
   tags:
     description: "Tags to pass as argument for nf-test --tag parameter"
     required: false
+  all_tests:
+    description: "Count all tagged tests instead of only those changed since HEAD^ (used for snapshot regeneration)"
+    required: false
+    default: "false"
 outputs:
   shard:
     description: "Array of shard numbers"
@@ -21,20 +25,24 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
       id: shards
       shell: bash
       run: |
         # Run nf-test with dynamic parameter
+        # In all_tests mode (snapshot regeneration) count every tagged test,
+        # not just those changed since HEAD^.
+        CHANGED_SINCE="--changed-since HEAD^"
+        if [ "${{ inputs.all_tests }}" = "true" ]; then CHANGED_SINCE=""; fi
         nftest_output=$(nf-test test \
           --profile +docker \
           $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
           --dry-run \
           --ci \
-          --changed-since HEAD^) || {
+          $CHANGED_SINCE) || {
             echo "nf-test command failed with exit code $?"
             echo "Full output: $nftest_output"
             exit 1

.github/actions/nf-test/action.yml

@@ -16,28 +16,32 @@ inputs:
   tags:
     description: "Tags to pass as argument for nf-test --tag parameter"
     required: false
+  update_snapshots:
+    description: "Run with --update-snapshot over all tagged tests and upload regenerated snapshots as artifacts"
+    required: false
+    default: "false"
 runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
       with:
         python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,7 +52,7 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba
@@ -71,18 +75,51 @@ runs:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
       run: |
+        # In update-snapshot mode, regenerate snapshots over ALL tagged tests
+        # (drop --changed-since, which is only meaningful for PR/push diffs).
+        CHANGED_SINCE="--changed-since HEAD^"
+        UPDATE_SNAPSHOT=""
+        if [ "${{ inputs.update_snapshots }}" = "true" ]; then
+          CHANGED_SINCE=""
+          UPDATE_SNAPSHOT="--update-snapshot"
+        fi
         nf-test test \
           --profile=+${{ inputs.profile }} \
           $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
           --ci \
-          --changed-since HEAD^ \
+          $CHANGED_SINCE \
+          $UPDATE_SNAPSHOT \
           --verbose \
           --tap=test.tap \
           --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
 
           # Save the absolute path of the test.tap file to the output
           echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
 
+    # ---- update-snapshot mode: collect & upload regenerated snapshots ----
+    # Only the canonical docker + pinned-Nextflow leg uploads, to avoid
+    # profile/version-specific artifact collisions.
+    - name: Collect updated snapshots
+      if: ${{ inputs.update_snapshots == 'true' && inputs.profile == 'docker' && env.NXF_VERSION == '25.10.4' }}
+      shell: bash
+      run: |
+        rm -rf updated-snaps && mkdir -p updated-snaps
+        git diff --name-only -- 'tests/*.snap' | while read -r f; do
+          mkdir -p "updated-snaps/$(dirname "$f")"
+          cp "$f" "updated-snaps/$f"
+        done
+        echo "Changed snapshot files (shard ${{ inputs.shard }}/${{ inputs.total_shards }}):"
+        git diff --name-only -- 'tests/*.snap' || true
+
+    - name: Upload updated snapshots
+      if: ${{ inputs.update_snapshots == 'true' && inputs.profile == 'docker' && env.NXF_VERSION == '25.10.4' }}
+      uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+      with:
+        name: updated-snapshots-shard-${{ inputs.shard }}
+        path: updated-snaps/
+        if-no-files-found: ignore
+        retention-days: 5
+
     - name: Generate test summary
       if: always()
       shell: bash

.github/workflows/cloudtest.yml → .github/workflows/awsfulltest.yml

@@ -1,8 +1,7 @@
-name: nf-core cloud tests (both full size and smaller)
+name: nf-core AWS full size tests
 # This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_full' on cloud
-# or the -profile 'test' on cloud (smaller tests)
+# It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request_review:
@@ -11,10 +10,6 @@ on:
     types: [published]
   workflow_dispatch:
     inputs:
-      test:
-        description: "-profile test (smaller)"
-        type: boolean
-        default: true
       somatic:
         description: "Somatic full test"
         type: boolean
@@ -41,12 +36,6 @@ jobs:
         run: |
           # All available profiles
           all='[
-            {
-              "profile": "test_aws",
-              "test": "test",
-              "compute_env": "TOWER_COMPUTE_ENV",
-              "workdir": "TOWER_BUCKET_AWS"
-            },
             {
               "profile": "test_full_aws",
               "test": "somatic",
@@ -70,7 +59,6 @@ jobs:
           if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
             # Filter to only selected profiles
             matrix=$(echo "$all" | jq -c '[.[] | select(
-              (.test == "test" and ${{ inputs.test }}) or
               (.test == "somatic" and ${{ inputs.somatic }}) or
               (.test == "germline" and ${{ inputs.germline }}) or
               (.test == "germline_ncbench_agilent" and ${{ inputs.germline_ncbench_agilent }})
@@ -98,7 +86,7 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         id: tower-launch
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
           run_name: sarek_${{ matrix.profile }}
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -141,9 +129,9 @@ jobs:
             --repo ${{ github.repository }} \
             --body "Cloud test **${{ matrix.profile }}** launched on [Seqera Platform](${{ steps.tower-launch.outputs.workflowUrl }})"
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file - ${{ matrix.profile }}
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -0,0 +1,33 @@
+name: nf-core AWS test
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
+
+on:
+  workflow_dispatch:
+jobs:
+  run-platform:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/sarek'
+    runs-on: ubuntu-latest
+    steps:
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
+        with:
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}
+          parameters: |
+            {
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
+            }
+          profiles: test
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: Seqera Platform debug log file
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         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."