Add testing of SpatialData output

nf-core · Mar 7, 2024 · d5f16b4 · d5f16b4
1 parent 3245e17
commit d5f16b4
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/tests/pipeline/test_downstream.nf.test b/tests/pipeline/test_downstream.nf.test
@@ -1,4 +1,4 @@
-extflow_pipeline {
+nextflow_pipeline {
     name "Test downstream workflow (excl. Space Ranger)"
     script "main.nf"
     tag "pipeline"
@@ -20,19 +20,21 @@ extflow_pipeline {
 
         then {
             assertAll(
+
                 // Workflow
                 { assert workflow.success },
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("nf_core_pipeline_software_mqc_versions.yml") },
 
                 // Data
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() },
+                { assert path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_sdata_processed.zarr").exists() },
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2.2/data/st_adata_processed.h5ad").exists() },
+                { assert path("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2.2/data/st_sdata_processed.zarr").exists() },
 
                 // Reports
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_quality_controls.html").text.contains("final results of all the filtering") },
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_clustering.html").text.contains("spatial distribution of clusters") },
-                { assert
-                file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_svg.html").text.contains("Spatial transcriptomics data can give insight") },
+                { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_svg.html").text.contains("Spatial transcriptomics data can give insight") },
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2.2/reports/st_quality_controls.html").text.contains("final results of all the filtering") },
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2.2/reports/st_clustering.html").text.contains("spatial distribution of clusters") },
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2.2/reports/st_svg.html").text.contains("Spatial transcriptomics data can give insight") },

diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test
@@ -24,6 +24,7 @@ nextflow_pipeline {
 
                 // Data
                 { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_adata_processed.h5ad").exists() },
+                { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/data/st_sdata_processed.zarr").exists() },
 
                 // Reports
                 { assert file("$outputDir/Visium_FFPE_Human_Ovarian_Cancer/reports/st_quality_controls.html").text.contains("final results of all the filtering") },

diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test
@@ -20,6 +20,7 @@ nextflow_pipeline {
 
                 // Data
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_adata_processed.h5ad").exists() },
+                { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/data/st_sdata_processed.zarr").exists() },
 
                 // Reports
                 { assert file("$outputDir/CytAssist_11mm_FFPE_Human_Glioblastoma_2/reports/st_quality_controls.html").text.contains("final results of all the filtering") },