ARM Megatests

.github/workflows/cloud_tests_full.yml

@@ -22,25 +22,26 @@ jobs:
     strategy:
       matrix:
         aligner: ["star_salmon", "star_rsem"]
+        arch: ["arm64", "x86_64"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
+          compute_env: ${{ matrix.arch == 'arm64' && secrets.TOWER_CE_AWS_CPU_ARM64 || secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
+          run_name: "aws_rnaseq_full_${{ matrix.aligner }}_${{ matrix.arch }}"
           revision: ${{ github.sha }}
-          profiles: test_full_aws
+          profiles: test_full_aws${{ matrix.arch == 'arm64' && ',docker_arm' || '' }}
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
                 "aligner": "${{ matrix.aligner }}",
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/${{ matrix.arch }}/aligner_${{ matrix.aligner }}/"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Tower_debug_action-${{ matrix.aligner }}-${{ matrix.arch }}.log
           path: tower_action_*.log
 
   run-full-tests-on-azure:
@@ -66,7 +67,7 @@ jobs:
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
                 "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: tower_action_*.log
@@ -93,7 +94,7 @@ jobs:
                 "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: tower_action_*.log

.github/workflows/cloud_tests_small.yml

@@ -17,21 +17,25 @@ jobs:
   run-small-tests-on-aws:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["star_salmon", "star_rsem"]
+        arch: ["arm64", "x86_64"]
     steps:
       - uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
+          compute_env: ${{ matrix.arch == 'arm64' && secrets.TOWER_CE_AWS_CPU_ARM64 || secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
-          run_name: "aws_rnaseq_small"
+          run_name: "aws_rnaseq_small_${{ matrix.arch }}"
           revision: ${{ github.sha }}
-          profiles: test
+          profiles: test${{ matrix.arch == 'arm64' && ',docker_arm' || '' }}
           parameters: |
             {
-                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}/"
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}/${{ matrix.arch }}/aligner_${{ matrix.aligner }}/"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: tower_action_*.log
@@ -53,7 +57,7 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: tower_action_*.log
@@ -75,7 +79,7 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
             }
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: tower_action_*.log

.github/workflows/containers_config.yml

@@ -0,0 +1,51 @@
+name: Container Configs
+
+on:
+  # FIXME Remove these and only run on release or PRs to main or TEMPLATE updates
+  push:
+    branches: [main,dev]
+  pull_request:
+    branches: [main,dev]
+  release:
+    types: [published]
+  # TODO workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      FORCE_COLOR: 1
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+          ref: ${{ github.head_ref }}
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: "25.01.0-edge"
+      - name: Snapshot containers
+        run: |
+          mkdir -p conf/containers
+          for container in docker singularity; do
+            for arch in amd64 arm64; do
+              if [ "$arch" = "arm64" ]; then
+                profile="wave,$container,arm"
+              else
+                profile="wave,$container"
+              fi
+              nextflow inspect . -profile $profile -format config > conf/containers/containers_${container}_${arch}.config
+              echo "Created conf/containers/containers_${container}_${arch}.config"
+              sort -o conf/containers/containers_${container}_${arch}.config conf/containers/containers_${container}_${arch}.config
+            done
+          done
+      - name: Commit & push changes
+        id: commit-and-push
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add conf/containers/.
+          git status
+          git commit -m "[automated] Update container configs"
+          git push
+