diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
index d4eb52b1e7a..823e7006498 100644
--- a/.github/workflows/api.yaml
+++ b/.github/workflows/api.yaml
@@ -56,8 +56,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -api
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: api
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/api_paste.yaml b/.github/workflows/api_paste.yaml
index 989cf1c0df4..9736a500a48 100644
--- a/.github/workflows/api_paste.yaml
+++ b/.github/workflows/api_paste.yaml
@@ -57,8 +57,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api-paste
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -api
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: api-paste
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
index 9e5cf7bdbb7..cd519f7779e 100644
--- a/.github/workflows/cwl_conformance.yaml
+++ b/.github/workflows/cwl_conformance.yaml
@@ -56,8 +56,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Run tests
-        run: ./run_tests.sh --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
+        run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: cwl-conformance
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
index c0c3b997428..620ddde62cd 100644
--- a/.github/workflows/framework.yaml
+++ b/.github/workflows/framework.yaml
@@ -54,8 +54,12 @@ jobs:
           path: .venv
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
       - name: Run tests
-        run: ./run_tests.sh --framework
+        run: ./run_tests.sh --coverage --framework
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 25bb0d3783a..e60259db46e 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -81,8 +81,12 @@ jobs:
       - name: Run tests
         run: |
           . .ci/minikube-test-setup/start_services.sh
-          ./run_tests.sh -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
+          ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml
index 6ee668d9517..20cbd35f226 100644
--- a/.github/workflows/integration_selenium.yaml
+++ b/.github/workflows/integration_selenium.yaml
@@ -60,8 +60,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -integration test/integration_selenium
+        run: ./run_tests.sh --coverage -integration test/integration_selenium
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration-selenium
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
index 844f4cc0495..6e4ed04764b 100644
--- a/.github/workflows/selenium.yaml
+++ b/.github/workflows/selenium.yaml
@@ -61,8 +61,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/selenium_beta.yaml b/.github/workflows/selenium_beta.yaml
index 5eeb2a8dab3..a32a9539f66 100644
--- a/.github/workflows/selenium_beta.yaml
+++ b/.github/workflows/selenium_beta.yaml
@@ -62,8 +62,12 @@ jobs:
           yarn-lock-file: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@master
       - name: Run tests
-        run: ./run_tests.sh -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium-beta-history
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
index 510d09c0469..9302fb9bcd7 100644
--- a/.github/workflows/unit.yaml
+++ b/.github/workflows/unit.yaml
@@ -44,11 +44,13 @@ jobs:
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit
       - name: Install ffmpeg
         run: sudo apt-get update && sudo apt-get -y install ffmpeg
-      - name: Install tox
-        run: pip install tox
       - name: Run tests
-        run: tox -e unit
+        run: ./run_tests.sh --coverage -u
         working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: py-unit
+          working-directory: 'galaxy root'
       - uses: actions/upload-artifact@v2
         if: failure()
         with:
diff --git a/run_tests.sh b/run_tests.sh
index 2aea9c68718..1ae213ac785 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -644,7 +644,7 @@ fi
 export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
     if [ "$coverage_arg" = '--with-coverage' ]; then
-        coverage_arg="--cov-report term --cov=lib"
+        coverage_arg="--cov-report xml --cov-report term --cov=lib"
     fi
     if [ -n "$marker" ]; then
         marker_args=(-m "$marker")