diff --git a/CHANGELOG.md b/CHANGELOG.md
index b1c5463a9..80b142345 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@
 - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- test pipeline with conda and singularity on PRs to master ([#3149](https://github.com/nf-core/tools/pull/3149))
 - run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
 - Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168))
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 06371cc97..eefb59496 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -7,6 +7,7 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
@@ -38,9 +39,21 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Run pipeline with test data (docker)
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+      - name: Run pipeline with test data (singularity)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
+        if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"
+
+      - name: Run pipeline with test data (conda)
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results
+        if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}"