Update pipeline-level test snapshots

Author: nictru

tests/default.nf.test.snap

@@ -21,6 +21,9 @@
                     "pandas": "2.2.3",
                     "seurat": "5.1.0"
                 },
+                "ADATA_TORDS": {
+                    "anndataR": "1.0.2"
+                },
                 "ADATA_UNIFY": {
                     "anndata": "0.12.7",
                     "numpy": "2.4.0",
@@ -245,6 +248,7 @@
                 "combine/merge/upset_genes.png",
                 "finalized",
                 "finalized/merged.h5ad",
+                "finalized/merged.rds",
                 "finalized/merged_metadata.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -283,10 +287,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
-        "timestamp": "2026-03-13T21:22:47.601973",
+        "timestamp": "2026-03-14T21:43:40.326384543",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         }
     }
 }

tests/main_pipeline_build.nf.test.snap

@@ -21,6 +21,9 @@
                     "pandas": "2.2.3",
                     "seurat": "5.1.0"
                 },
+                "ADATA_TORDS": {
+                    "anndataR": "1.0.2"
+                },
                 "ADATA_UNIFY": {
                     "anndata": "0.12.7",
                     "numpy": "2.4.0",
@@ -259,6 +262,7 @@
                 "combine/merge/upset_genes.png",
                 "finalized",
                 "finalized/merged.h5ad",
+                "finalized/merged.rds",
                 "finalized/merged_metadata.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -297,10 +301,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
-        "timestamp": "2026-03-14T19:09:42.838981",
+        "timestamp": "2026-03-14T22:00:59.334514797",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         }
     }
 }

tests/main_pipeline_extend.nf.test.snap

@@ -18,6 +18,9 @@
                     "anndata": "0.12.7",
                     "python": "3.13.11"
                 },
+                "ADATA_TORDS": {
+                    "anndataR": "1.0.2"
+                },
                 "ADATA_UNIFY": {
                     "anndata": "0.12.7",
                     "numpy": "2.4.0",
@@ -179,6 +182,7 @@
                 "combine/merge",
                 "finalized",
                 "finalized/merged.h5ad",
+                "finalized/merged.rds",
                 "finalized/merged_metadata.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -213,10 +217,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
-        "timestamp": "2026-03-14T19:21:25.557709",
+        "timestamp": "2026-03-14T21:42:56.024699134",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         }
     }
 }

tests/main_pipeline_reference_mapping.nf.test.snap

@@ -14,6 +14,9 @@
                     "scanpy": "1.11.5",
                     "scipy": "1.16.3"
                 },
+                "ADATA_TORDS": {
+                    "anndataR": "1.0.2"
+                },
                 "ADATA_UNIFY": {
                     "anndata": "0.12.7",
                     "numpy": "2.4.0",
@@ -179,6 +182,7 @@
                 "combine/merge",
                 "finalized",
                 "finalized/merged.h5ad",
+                "finalized/merged.rds",
                 "finalized/merged_metadata.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -213,10 +217,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
-        "timestamp": "2026-03-14T14:53:34.369624",
+        "timestamp": "2026-03-14T21:40:38.750227073",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         }
     }
 }

tests/main_pipeline_sub.nf.test.snap

@@ -1,7 +1,7 @@
 {
     "Should be able to perform subclustering": {
         "content": [
-            289,
+            290,
             {
                 "ADATA_EXTEND": {
                     "anndata": "0.12.7",
@@ -13,6 +13,9 @@
                     "anndata": "0.12.7",
                     "python": "3.13.11"
                 },
+                "ADATA_TORDS": {
+                    "anndataR": "1.0.2"
+                },
                 "ENTROPY": {
                     "python": "3.13.11",
                     "scanpy": "1.11.5",
@@ -107,6 +110,7 @@
                 "cluster_dimred/scvi/umap",
                 "finalized",
                 "finalized/base.h5ad",
+                "finalized/base.rds",
                 "finalized/base_metadata.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
@@ -587,10 +591,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
-        "timestamp": "2026-03-14T20:17:44.297436",
+        "timestamp": "2026-03-14T21:33:52.663299912",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         }
     }
 }