update tests to include all tools

.github/workflows/test_run_dataset_R.yml

@@ -68,4 +68,4 @@ jobs:
         run: |
           echo $(ls)
           Rscript unit-test/test_run_dataset.R \
-          rctd,music,spatialdwls
+          rctd,music,spatialdwls,nnls,seurat

.github/workflows/test_run_dataset_dstg.yml

@@ -0,0 +1,68 @@
+name: test run_dataset mode - dstg
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [pull_request, workflow_dispatch ]
+
+jobs:
+  run_dataset:
+    name: Run workflow with run_dataset mode
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: 
+          - 'NXF_VER=21.04.3'
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+        # with:
+        #   lfs: true
+
+      - name: Download test dataset
+        run: |
+          wget https://zenodo.org/record/5763377/files/test_data.tar.gz?download=1 -O test_data.tar.gz
+          tar -xzvf test_data.tar.gz
+          echo $(ls)
+
+  #     - name: Checkout LFS objects
+  #       run: git lfs checkout
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
+
+      - name: Run pipeline with test data
+        run: |
+          nextflow run main.nf -profile test,docker --mode run_dataset \
+          --methods dstg
+
+      - name: Upload proportions and metrics
+        uses: actions/upload-artifact@v3
+        with:
+          name: deconv-proportions-and-metrics
+          path: |
+            deconv_proportions/*
+            results/*
+            trace.txt
+
+  test_output_run_dataset:
+    name: Tests outputs of the pipeline
+    needs: run_dataset
+    runs-on: ubuntu-latest
+    container: rocker/tidyverse:3.6.3
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Download proportions from test run
+        uses: actions/download-artifact@v3
+        with:
+          name: deconv-proportions-and-metrics
+
+      - name: Check proportions and metrics with testthat
+        shell: bash
+        run: |
+          echo $(ls)
+          Rscript unit-test/test_run_dataset.R dstg

.github/workflows/test_run_dataset_python.yml

@@ -1,4 +1,4 @@
-name: test run_dataset mode
+name: test run_dataset mode for Python tools
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on: [ pull_request, workflow_dispatch ]
 
@@ -36,7 +36,7 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run main.nf -profile test,docker --mode run_dataset \
-          --methods cell2location,stereoscope,destvi
+          --methods cell2location,stereoscope,destvi,tangram,stride
 
       - name: Upload proportions and metrics
         uses: actions/upload-artifact@v3
@@ -66,4 +66,4 @@ jobs:
         run: |
           echo $(ls)
           Rscript unit-test/test_run_dataset.R \
-          cell2location,stereoscope,destvi
+          cell2location,stereoscope,destvi,tangram,stride

.github/workflows/test_run_dataset_spotlight.yml

@@ -1,4 +1,4 @@
-name: test run_dataset mode
+name: test run_dataset mode - spotlight
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on: [pull_request, workflow_dispatch ]
 

conf/test.config

@@ -16,7 +16,9 @@ params {
     deconv_args = [spotlight: "--logfc.threshold 0.25 --min.pct 0.1",
                     cell2location: [build: "-p 10", fit: "-p 10 -n 30"],
                     stereoscope: "-n 5000",
-                    destvi: []]
+                    destvi: [],
+                    dstg: [dir: ""],
+                    stride: "--ntopics 20"]
 
     synthspot = [sc_input: "unit-test/test_sc_data.rds",
               clust_var: "subclass",

unit-test/test_run_dataset/metrics_cell2location_test_sp_data

@@ -1,2 +1,2 @@
-"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc"
-0.110622360090902 0.100663167915726 0.207 0.5 1 0 0.207 0.343 0.566 0.275883464348976
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.110642599743902 0.10066314583284 0.207 0.5 1 0 0.207 0.343 0.566 0.275917367241725 0.582912761355442 0.61888617039506

unit-test/test_run_dataset/metrics_destvi_test_sp_data

@@ -1,2 +1,2 @@
-"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc"
-0.0145696592201077 0.101729783953808 0.207 0.5 1 0 0.207 0.343 0.566 0.2192500796612
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.014569664254185 0.101729783780696 0.207 0.5 1 0 0.207 0.343 0.566 0.2192500796612 0.504506128334536 0.626149897957899

unit-test/test_run_dataset/metrics_dstg_test_sp_data

@@ -0,0 +1,2 @@
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.680519179784906 0.0682051290374751 0.367 0.601 1 0.202 0.246 0.395 0.62 0.699914632736589 0.879551189617876 0.317108568421564

unit-test/test_run_dataset/metrics_spotlight_test_sp_data

@@ -1,2 +1,2 @@
-"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc"
-0.865593803191432 0.0523936246671797 0.524 0.686 0.961 0.411 0.298 0.455 0.665 0.90028650805289
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.865593803191432 0.0523936246671797 0.524 0.686 0.961 0.411 0.298 0.455 0.665 0.900242143795783 0.936418529199713 0.224147894488034

unit-test/test_run_dataset/metrics_stereoscope_test_sp_data

@@ -1,2 +1,2 @@
-"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc"
-0.0110282994161923 0.104999613513269 0.217 0.502 0.987 0.017 0.207 0.342 0.563 0.206284339597483
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.0110282963938356 0.104999613443245 0.217 0.502 0.987 0.017 0.207 0.342 0.563 0.206284339597483 0.512436914203316 0.644602335090136

unit-test/test_run_dataset/metrics_stride_test_sp_data

@@ -0,0 +1,2 @@
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.54223410865828 0.091716447911441 0.595 0.691 0.855 0.527 0.32 0.466 0.641 0.553426086385818 0.77460346070656 0.401417602891877

unit-test/test_run_dataset/metrics_tangram_test_sp_data

@@ -0,0 +1,2 @@
+"corr" "RMSE" "accuracy" "balanced_accuracy" "sensitivity" "specificity" "precision" "F1" "F2" "prc" "roc" "jsd"
+0.771419110743224 0.0644334125870186 0.796 0.808 0.829 0.788 0.504 0.627 0.734 0.794897985371974 0.897981254506127 0.206574602899636