Preserve reads filtered out at dada2 filterAndTrim

.github/workflows/docker-publish.yml → .github/workflows/publish-tag.yml

@@ -1,4 +1,4 @@
-name: Build and push docker image
+name: Build and push docker image from tag
 
 on:
   push:
@@ -15,21 +15,20 @@ jobs:
         run: env
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push on git tag event
         if: github.ref_type == 'tag'
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: "{{defaultContext}}:docker"
           push: true
           tags: |
-            ghcr.io/${{ github.repository }}:latest
             ghcr.io/${{ github.repository }}:${{ github.ref_name }}

.github/workflows/tests.yml

@@ -1,18 +1,19 @@
 name: Run pipeline tests on PRs
 
-on: [push, pull_request]
+on: push
 
 jobs:
   test:
+    needs: [latest_image]
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/nhoffman/dada2-nf:latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-java@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-java@v4
       with:
         distribution: 'temurin'
-        java-version: '17'
+        java-version: '21'
     - run: |
         cd /usr/local/bin/
         wget -qO - https://github.com/nextflow-io/nextflow/releases/download/v22.10.8/nextflow | bash