update the number of tasks that are executed, and include raw/filtere…

…d in the testings (cellranger)
nf-core · Feb 14, 2024 · 2d7c90e · 2d7c90e
1 parent c539399
commit 2d7c90e
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/tests/main_pipeline_cellranger.test b/tests/main_pipeline_cellranger.test
@@ -30,21 +30,23 @@ nextflow_pipeline {
                 {assert workflow.success},
 
                 // How many tasks were executed?
-                {assert workflow.trace.tasks().size() == 15},
+                {assert workflow.trace.tasks().size() == 20},
 
                 // How many results were produced?
                 {assert path("${outputDir}/results_cellranger").list().size() == 4},
                 {assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4},
-                {assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4},
+                {assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 5},
                 {assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3},
                 {assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12},
                 {assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3},
 
                 //
                 // Check if files were produced
                 //
-                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
-                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_raw_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_filtered_matrix.h5ad" ).exists()},
+                {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_filtered_matrix.h5ad" ).exists()},
 
                 //
                 // Check if files are the same
@@ -63,8 +65,10 @@ nextflow_pipeline {
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ),
                     path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
-                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
-                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_raw_matrix.rds" ),
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_filtered_matrix.rds" ),
+                    path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_filtered_matrix.rds" )
                 ).match()}
 
             ) // end of assertAll()

diff --git a/tests/main_pipeline_cellranger.test.snap b/tests/main_pipeline_cellranger.test.snap
@@ -14,8 +14,8 @@
                 "errorMessage": "",
                 "trace": {
                     "tasksFailed": 0,
-                    "tasksCount": 15,
-                    "tasksSucceeded": 15
+                    "tasksCount": 20,
+                    "tasksSucceeded": 20
                 },
                 "name": "workflow",
                 "success": true
@@ -32,9 +32,15 @@
             "barcodes.tsv.gz:md5,081f72b5252ccaf5ffd535ffbd235c4c",
             "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
             "matrix.mtx.gz:md5,a4db04e43e650accc96361a287126a6b",
-            "Sample_X_matrix.rds:md5,f9191ba575a3ab79ada4807715f18573",
-            "Sample_Y_matrix.rds:md5,7be3f7b29d668dcf7e951b9f4d371a5e"
+            "Sample_X_raw_matrix.rds:md5,306a5477ace4d43d851b8389fdfeaf1f",
+            "Sample_Y_raw_matrix.rds:md5,74b31532da4cae5a8197d690021d77fc",
+            "Sample_X_filtered_matrix.rds:md5,f9191ba575a3ab79ada4807715f18573",
+            "Sample_Y_filtered_matrix.rds:md5,7be3f7b29d668dcf7e951b9f4d371a5e"
         ],
-        "timestamp": "2024-01-22T15:19:20.134275449"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-14T15:10:31.638485641"
     }
 }