diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 08622fd5..ad2f1283 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,7 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
@@ -65,8 +67,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --skip_qiime --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --skip_qiime --outdir ./results
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2a14c0e0..0a6c5837 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#718](https://github.com/nf-core/ampliseq/pull/718) - Require a minimum sequence length of 50bp for taxonomic classifcation after using ITSx
 - [#721](https://github.com/nf-core/ampliseq/pull/721) - Fix error `unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException` caused by a missing `\` in nf-core module `pigz/uncompress` (which had no consequences but was confusing)
 - [#722](https://github.com/nf-core/ampliseq/pull/722) - When barrnap detects several genes select the lowest e-value
+- [#726](https://github.com/nf-core/ampliseq/pull/726) - Add fallback to `download_pipeline.yml` because the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))
 
 ### `Dependencies`