diff --git a/.github/workflows/test_run_dataset_R.yml b/.github/workflows/test_run_dataset_R.yml index 37ec7fb..3835c82 100644 --- a/.github/workflows/test_run_dataset_R.yml +++ b/.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 \ No newline at end of file + rctd,music,spatialdwls,nnls,seurat \ No newline at end of file diff --git a/.github/workflows/test_run_dataset_dstg.yml b/.github/workflows/test_run_dataset_dstg.yml new file mode 100644 index 0000000..af4b1eb --- /dev/null +++ b/.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 \ No newline at end of file diff --git a/.github/workflows/test_run_dataset_python.yml b/.github/workflows/test_run_dataset_python.yml index e02e073..7e26597 100644 --- a/.github/workflows/test_run_dataset_python.yml +++ b/.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 \ No newline at end of file + cell2location,stereoscope,destvi,tangram,stride \ No newline at end of file diff --git a/.github/workflows/test_run_dataset_spotlight.yml b/.github/workflows/test_run_dataset_spotlight.yml index 3084b4b..73d4d27 100644 --- a/.github/workflows/test_run_dataset_spotlight.yml +++ b/.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 ] diff --git a/conf/test.config b/conf/test.config index da16b5b..a1a7a1a 100644 --- a/conf/test.config +++ b/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", diff --git a/unit-test/test_run_dataset/metrics_cell2location_test_sp_data b/unit-test/test_run_dataset/metrics_cell2location_test_sp_data index b399a48..3518baa 100644 --- a/unit-test/test_run_dataset/metrics_cell2location_test_sp_data +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_destvi_test_sp_data b/unit-test/test_run_dataset/metrics_destvi_test_sp_data index 951bc1d..f88bd67 100644 --- a/unit-test/test_run_dataset/metrics_destvi_test_sp_data +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_dstg_test_sp_data b/unit-test/test_run_dataset/metrics_dstg_test_sp_data new file mode 100644 index 0000000..574ff33 --- /dev/null +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_spotlight_test_sp_data b/unit-test/test_run_dataset/metrics_spotlight_test_sp_data index ed5ee4a..ac36fa6 100644 --- a/unit-test/test_run_dataset/metrics_spotlight_test_sp_data +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_stereoscope_test_sp_data b/unit-test/test_run_dataset/metrics_stereoscope_test_sp_data index fb7245e..9022180 100644 --- a/unit-test/test_run_dataset/metrics_stereoscope_test_sp_data +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_stride_test_sp_data b/unit-test/test_run_dataset/metrics_stride_test_sp_data new file mode 100644 index 0000000..921c513 --- /dev/null +++ b/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 diff --git a/unit-test/test_run_dataset/metrics_tangram_test_sp_data b/unit-test/test_run_dataset/metrics_tangram_test_sp_data new file mode 100644 index 0000000..dab7abf --- /dev/null +++ b/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 diff --git a/unit-test/test_run_dataset/proportions_cell2location_test_sp_data b/unit-test/test_run_dataset/proportions_cell2location_test_sp_data index 6c4956e..888d108 100644 --- a/unit-test/test_run_dataset/proportions_cell2location_test_sp_data +++ b/unit-test/test_run_dataset/proportions_cell2location_test_sp_data @@ -1,17 +1,17 @@ Astro CR Endo L23IT L4 L5IT L5PT L6b L6CT L6IT Lamp5 Macrophage Meis2 NP Oligo Peri Pvalb Serpinf1 SMC Sncg Sst Vip VLMC -0.045017257450461 0.0449574010026478 0.0428074715872374 0.0446030112744983 0.0434294288533389 0.0441921505459543 0.0429024649538775 0.0444847853179534 0.0433095987658398 0.0427898005580566 0.0431407839807843 0.0441952540877858 0.0430252368799268 0.0423226984821823 0.0421720381159035 0.0432175480978739 0.0422334690203987 0.042816440313507 0.04333990673442 0.0427245707016085 0.0430688696719443 0.0440036830063997 0.0452461305974002 -0.042391378632358 0.0429203158894981 0.0440963956359926 0.0427074540574454 0.0433368223986089 0.0425184447553973 0.043345209629782 0.043214826601477 0.0423235478660214 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a/unit-test/test_run_dataset/proportions_stereoscope_test_sp_data b/unit-test/test_run_dataset/proportions_stereoscope_test_sp_data index d82fd7a..8a448d0 100644 --- a/unit-test/test_run_dataset/proportions_stereoscope_test_sp_data +++ b/unit-test/test_run_dataset/proportions_stereoscope_test_sp_data @@ -1,17 +1,17 @@ Astro CR Endo L23IT L4 L5IT L5PT L6b L6CT L6IT Lamp5 Macrophage Meis2 NP Oligo Peri Pvalb Serpinf1 SMC Sncg Sst Vip VLMC -0.09963572 0.015706748 0.031806152 0.051476724 0.016184058 0.020011108 0.08733114 0.06434061 0.02130298 0.02751449 0.024769366 0.04265754 0.033107854 0.093531914 0.01802448 0.037890274 0.02737979 0.0459864 0.018182665 0.12719135 0.020112256 0.02272467 0.05313177 -0.016468536 0.043868694 0.029234093 0.037823446 0.0041245758 0.05574633 0.06944328 0.09693298 0.017922314 0.043645523 0.07859319 0.008731359 0.06743112 0.036819115 0.059795335 0.052754525 0.021374598 0.006278466 0.023043213 0.08503934 0.08462518 0.008772331 0.05153258 -0.028966228 0.026561337 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0.036084484 0.011679565 0.06463868 0.017403735 0.082437806 diff --git a/unit-test/test_run_dataset/proportions_stride_test_sp_data b/unit-test/test_run_dataset/proportions_stride_test_sp_data new file mode 100644 index 0000000..a48561a --- /dev/null +++ b/unit-test/test_run_dataset/proportions_stride_test_sp_data @@ -0,0 +1,17 @@ +Astro CR Endo L23IT L4 L5IT L5PT L6b L6CT L6IT Lamp5 Macrophage Meis2 NP Oligo Peri Pvalb Serpinf1 SMC Sncg Sst Vip VLMC +0 0.0381024714574242 0.133310203049045 0.0481656856712616 0.046799102846388 0.0558724169585164 0.051224019773469 0.0835348746327741 0.0650148197655119 0.0541942710763068 0.0409976763207672 0.00152778079029021 0.0363374828241475 0.0563775206878527 0 0.0233542741024088 0.0416669436642305 0.0231703018876378 0.131978490905652 0.0152758904627979 0.048571472948007 0.00319193018257506 0.00133236999293617 +0.069501968046098 0.0672848976505818 0.0143251905660604 0.0221375114031283 0.0402047567051333 0.00695121379353643 0.00808838612463658 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