diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2d0c83301d..c2065a447e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Template
 
 * Move TODO item of `contains:` map in a YAML string [[#1082](https://github.com/nf-core/tools/issues/1082)]
+* Trigger AWS tests via Tower API [[#1160](https://github.com/nf-core/tools/pull/1160)]
 
 ### General
 
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index c033c7756c..9ec98b29f9 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -1,45 +1,34 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   release:
     types: [published]
   workflow_dispatch:
-
-{% raw %}
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-{% endraw %}
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS full tests
     if: github.repository == '{{ name }}'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
-        run: |
-          aws batch submit-job \
-            --region eu-west-1 \
-            --job-name nf-core-{{ short_name }} \
-            --job-queue $AWS_JOB_QUEUE \
-            --job-definition $AWS_JOB_DEFINITION \
-            --container-overrides '{"command": ["{{ name }}", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/{{ short_name }}/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/{{ short_name }}/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+        {% raw %}
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
+          parameters: |
+            {
+              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
+            }
+          profiles: '[ "test_full", "aws_tower" ]'
+
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 38cb57d086..fff75db64c 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -1,42 +1,28 @@
 name: nf-core AWS test
-# This workflow is triggered on push to the master branch.
-# It can be additionally triggered manually with GitHub actions workflow dispatch.
-# It runs the -profile 'test' on AWS batch.
+# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
+# It runs the -profile 'test' on AWS batch
 
 on:
   workflow_dispatch:
-
-{% raw %}
-env:
-  AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-  AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-  TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
-  AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
-  AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
-  AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
-{% endraw %}
-
 jobs:
-  run-awstest:
+  run-tower:
     name: Run AWS tests
     if: github.repository == '{{ name }}'
     runs-on: ubuntu-latest
     steps:
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@master
+        {% raw %}
         with:
-          auto-update-conda: true
-          python-version: 3.7
-      - name: Install awscli
-        run: conda install -c conda-forge awscli
-      - name: Start AWS batch job
-        # 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: |
-          aws batch submit-job \
-          --region eu-west-1 \
-          --job-name nf-core-{{ short_name }} \
-          --job-queue $AWS_JOB_QUEUE \
-          --job-definition $AWS_JOB_DEFINITION \
-          --container-overrides '{"command": ["{{ name }}", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/{{ short_name }}/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/{{ short_name }}/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
+          parameters: |
+            {
+              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
+            }
+          profiles: '[ "test", "aws_tower" ]'
+