diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 9ae59945cb..9f07f7cbed 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -52,6 +52,7 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
+        submodules: true
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -76,6 +77,7 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 1
+        submodules: true
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -117,6 +119,7 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 1
+        submodules: true
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
@@ -193,6 +196,7 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 1
+        submodules: true
     - uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000000..a15abe233c
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows"]
+	path = workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows
+	url = https://github.com/ebi-gene-expression-group/scxa-workflows
diff --git a/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows
new file mode 160000
index 0000000000..12596848f8
--- /dev/null
+++ b/workflows/single-cell-RNAseq/.ebi-gene-expression-group/scxa-workflows
@@ -0,0 +1 @@
+Subproject commit 12596848f8f89ff0d46fbf196211a869a1ad1016
diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml
new file mode 100644
index 0000000000..0ba0b2c5aa
--- /dev/null
+++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/.dockstore.yml
@@ -0,0 +1,7 @@
+version: 0.2.4
+workflows:
+- name: 'SCXA prod v0.2.4, Scanpy 1.7.X'
+  primaryDescriptorPath: /SingleCellExpressionAtlas-smartseq.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /SingleCellExpressionAtlas-smartseq-test.yml
diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml
new file mode 100644
index 0000000000..b89c1f701b
--- /dev/null
+++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq-test.yml
@@ -0,0 +1,17 @@
+- doc: Test Single Cell Expression Atlas smartseq execution using E-MTAB-6077
+  job:
+    genemeta:
+      class: File
+      location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/Danio_rerio.GRCz11.99.gtf.gz
+    genes:
+      class: File
+      location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx_rows.gz
+    cellmeta:
+      class: File
+      location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.cell_metadata.tsv 
+    barcodes:
+      class: File
+      location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx_cols.gz
+    matrix:
+      class: File
+      location: http://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/E-MTAB-6077/E-MTAB-6077.aggregated_counts.mtx.gz
diff --git a/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga
new file mode 120000
index 0000000000..93dcd6df76
--- /dev/null
+++ b/workflows/single-cell-RNAseq/SingleCellExpressionAtlas-downstream/SingleCellExpressionAtlas-smartseq.ga
@@ -0,0 +1 @@
+../.ebi-gene-expression-group/scxa-workflows/w_smart-seq_clustering/scanpy_clustering_workflow.json
\ No newline at end of file